Eschalon Book II Skills

Eschalon Book II's skills are more specialized abilities than the "ability" scores, and will unlock the ability to do more specific things, like pick locks, brew potions, and cast magick spells.

Magickal Skills: Elemental & Divination (Intro)
There are two magickal disciplines in the Eschalon trilogy: Elemental Magick and Divination Magick. We wrote a separate section on them that includes a description of all their spells, but for a quick summary of our favorites in a zero kills pacifist run through Book II:
Our favorite Elemental spells were Sparkling Wonder (arguably the best spell in the game to repel hostile foes without causing them any harm), Dense Nimbus (which deflects projectiles enemies fire at you), and Invisibility.
Our favorite Divination spells were Haste (which enables you to move much faster than any foes) and Ogre Strength (which lets you dramatically increase your strength to carry away more treasure from hostile territory).

Training in Magick:
You'll have the ability to learn both disciplines of magick in Book II from Luci, the owner of the "Darkest Arts" magick shop in Port Kuudad. This means you can theoretically unlock all three tiers of spells in both disciplines by only investing a few more skill points from your own level-ups.

Elemental vs Divination Magick on a Pacifist Run:
Both disciplines are valuable, but if we had to choose only one to specialize in beyond level 8, Elemental was our top choice:
Divination has an Entangle spell that can be a lot of fun to cast on susceptible foes, but in practice Entangle often didn't work reliably (if at all) on tough enemies, whereas Elemental's tier 1 spell Sparkling Wonder usually worked at its highest casting level even on surprisingly high-level foes up to the end of the game.
Divination's level 1 healing spell is very useful, but at higher tiers, Divination spells are also more combat-oriented. Elemental also has the highly useful "Dense Nimbus" spell which is very effective at deflecting projectiles (which are often the biggest danger on a pacifist challenge run).
At high levels, specializing in Elemental will let your Invisibility spell last longer, and you can also use the useful Portal spell to teleport yourself across large distances (though not inside most dungeons).
Elemental also has a Trapkill and Lockmelt spell that allow you to bypass most locks and traps in the game without any rogue skills. This is extremely useful. (However, also be warned that you'll eventually still want solid lock picking skills before you reach the final stronghold in the game, where the Lock Melt spell won't work on at least two vital locks that you must open to win the whole game via a zero kill run.)

Also see the separate Eschalon Book II Magick section for more details, including a complete list of spells from Book II's two magick disciplines.

Rogue/Thief Skills: Pick Locks, Hiding in Shadows, and Moving Silently
Playing as a stealthy rogue in Eschalon Book I was much easier than in Book II, since the Hide in Shadows skill was balanced to be less overpowered. However, using stealth to stay concealed in the shadows and move silently is another viable way to win a pacifist run through Book II (and can also be learned as a supporting skill for a mage or any other type of character). 

Hide in Shadows & Move Silently (Stealth)
The Hide in Shadows skill lets you conceal yourself from enemies' view and move in dark areas unseen. It's a passive skill, so success depends significantly on your skill level and surrounding conditions.
The Move Silently skill enables you to move without being heard by nearby foes, who will remain unaware of your presence as long as they can't see you. (In Book I, it was easy to ignore this skill and still stay hidden in the shadows easily even if the sounds aggravated enemies, but in Books II and III both are probably necessary to stay hidden successfully.)
Move Silently (supported by higher dexterity) is more useful in Book II than it was in Book I, since Hide in Shadows is no longer as overpowered, and you probably will want plug points into both skills to use stealth optimally.

Pick Locks
This valuable pacifist run skill lets you open locked treasure chests and doors. You'll need one skill point to even be able to make an attempt, after which you'll have a percentage chance to succeed that increases with more skill levels in lockpicking, supported by your dexterity score.
Picking locks is also a valuable pacifist run skill because success will grant you a decent number of experience points every time you pick a lock, and you can keep trying after each failed attempt. (This can cause you to break a lot of lockpicks if your skill level is low, but you can keep trying for as long as you want as long as you have enough lockpicks.)
Last but not least, if you're playing as a pacifist-run mage: There are at least two locks near the very end of the game that the Lock Melt spell will not work on, which means you could get stuck if you don't have a decent number of skill points in picking locks. (The Lock Melt spell also won't award you any xp when you use it to melt a lock, but the Pick Lock skill will.)

Training in Stealth & Pick Locks: 
All three of these rogue/thief skills have the same trainer: Zeblin, who you'll find in the bottom of the dangerous Thieves' Arcadia. (This is a difficult area to get through as a low-level pacifist-run character unless you already have solid magick or stealth skill to get through it, which is another reason playing as a mage is probably at least a bit easier in Book II than starting out as a rogue character.)

Other Skills

This is one of our favorite Eschalon Book II pacifist run skills: It will enable you to combine two of many different types of alchemical reagents (which you can find, forage for, or buy from merchants) to brew many different types of potions. Many potions can grant you the same temporary abilities you'd otherwise only be able to get from higher-tier Elemental or Divination spells. Examples include Haste Potions, Invisibility Potions, Potions of Ogre Strength, and many others. Alchemy can also be used to brew your own Healing Elixirs and Mana Potions.
Training in Alchemy: You can train up to level 8 in Alchemy skill with Becka at Port Kuudad.
You can brew modest healing elixirs and mana potions with only a single skill point. The maximum you can train in without investing your own skill points is level 8 (enough to brew a modest invisibility potion), but you can also get a skill manual to add to that base + several "brewmaster" rings that increase your Alchemy skills even more. (In a pacifist run, this means you'll have the option to obtain fairly high levels of alchemy skill without having to invest scarce skill points from your own level-ups based on nonviolent questing xp.)

After you learn Foraging, your player character will automatically forage off-screen for alchemical reagents (e.g. Mandrake Roots, Willow Bark, Dwarven Mellowleaf, etc) whenever you camp, and when you break camp you'll find a sack with the reagents he found sitting on the ground, which you can just pick up and take with you. The higher your skill in foraging, the more valuable the reagents you find will be.
You can use the foraging skill to accumulate huge numbers of reagents that can be sold for gold, and/or brewed into powerful potions that can be either sold or kept for your own use.
Also keep your eye out for green "Ring of the Boar" items in magic shops, since they can increase your Foraging skill by several points per ring, with or without training. (Once you train up to level 8, this will add those additional points to your total Foraging skill.)

Foraging in Caves or Dungeons:
If you spend a long time camped outside, you'll sometimes be randomly interrupted by outlanders, wolves, and other unfriendly creatures, so you'd have to evade them and go find a new campsite if you're on a pacifist challenge run. However, there's another "secret" to foraging that you can use to your advantage: If you go make camp in a cave (or underground/dungeon area like the Old Convent Well in Eastwillow), you can camp for as long as you want without ever being disturbed. (We figured this out by climbing down the Old Convent Well in Eastwillow and making camp on the mossy patch right at the bottom of the ladder, after some rats chased us out of our foraging camp in the nearby woods in the west.) 
There is no time limit in the Eschalon games, so there's no limit to how many valuabe reagents you can find while Foraging in caves (which probably explains why the Foraging skill was radically revised to become less powerful in Book III).

Investing skill points in the Mercantile skill can substantially increase the amount of gold you get from selling anything from foraged alchemical reagents, to valuable magickal weapons or other treasures stolen from enemy strongholds or dungeons. (It will also reduce the markup that all merchants charge you when you buy items from them.) This will start to make a big difference even early on, but if you increase your Mercantile skill as high as level 20, you can sell items at their full value, which will soon result in a huge increase in gold as you go on selling treasures you've found or looted from enemy strongholds.
Items you buy from merchants in the Eschalon trilogy are often expensive, and gold is relatively scarce compared with many other RPGs (especially if you're a pacifist challenge who doesn't kill for gold), but this skill can help give you an advantage, and is great if you want to achieve the in-game "Wealthy Lord" achievement (as well as the in-game "The Pacifist" achievement).
Note: There is no Mercantile skill trainer in Book I or II, so the mercantile skill manual is worth reading right away as soon as you come across it. There are also "dealer hats" that you can find to give you several more points in Mercantile whenever you put one on, so you should probably keep an eye out for those even if you're not "a hat person."
Optional aside on "breaking" the Mercantile skill: We never "abused" the Mercantile skill in our runs and you could still win a pacifist run without even learning it, but we also tested and confirmed that mercantile can also become overpowered if you continued investing points beyond around level 23-4: If you increase the skill to around level 25, you can buy and sell items for the same price, turning every merchant's store into a sort of 0% interest lending shop in which you can sell back anything at the same price you purchased it for, even if you "borrow" and use it for as long as you want in the interim. (If you go beyond this to level 26-7 or higher, you could engage in the surreal process of buying any item from a merchant for its market value, and then immediately selling it back at a premium, so that the merchant gradually runs out of gold from trading the same item back and forth repeatedly.)

This skill lets you disarm traps that you've detected (which you'll have to do with some combination of the Perception ability and Spot Hidden skill level). While definitely useful, we rarely used this skill even when playing as a rogue, for several reasons: One is that there are already a lot of thief/rogue skill categories to plug points to, which means you'd be spreading them pretty thin by plugging lots of points to this one as well. Another reason is that there are alternative ways to get around most (if not all) traps: If you're an Elemental Mage, you can use a Trapkill spells to disable traps, and if your high Perception (and/or Spot Hidden skill, which you can get points in by wearing rings) enables you to spot a trap before it's disarmed, you can often also do things like throwing rocks or darts at a trapped chest from a distance until the trap is triggered. Then traps will harmlessly detonate without ever having to risk being slain while trying to disarm them, and you can walk right up afterward and open the chest. (Many minor traps also won't seriously harm you if you accidentally set them off— though that's definitely not always the case, and there are also a good number of traps that can easily kill you instantly if you don't do something to disarm them first.)

Spot Hidden
This skill enables you to detect traps and other hidden objects, like gemstones you can find inside the rock walls of caves. (These usually are not vital to find at any time in the game, but are a lot of fun to discover while treasure hunting.) Your chance to spot a hidden object is re-rolled continuously when you are walking around (or when standing still and passing turns), and you can also get a skill manual and several "Rings of the Hawk" that will grant you some more points in the skill. All this means you can get away with conserving skill points without training in this skill, since you can stand next to any chests that you suspect contain traps and pass turns (by hitting the spacebar) over and over again until your mage detects them. (If memory serves, you can also spot hidden objects just with a high Perception skill alone, which any pacifist mage will probably already have.)

This increases your natural rate of mana regeneration, which sounds important for a pacifist mage. However, we always found this skill unnecessary, since you can also gain rapid natural mana regeneration by optimizing your Perception attribute score. (You can start a new game with a substantial Perception score from the start, and rapidly increase it after only a few level gains, so it ends up somewhere between level 30-40 before you're even forced to get through any particularly formidable dungeon areas.) We always did things this way, but if you find a manual to learn Meditation without skill points, it's still a useful supporting skill.

This will impact your ability to identify unknown items. Doing this is important, since if you try to sell an unidentified item to any merchant in Eschalon, they'll tell you that the item "isn't worth much to them" and make you a lowball offer.
However, you can avoid wasting skill points on this skill by instead using the Divination "Lore" spell instead. (Even if you don't want to play as a Diviner on your pacifist run, you can train Divination Magick up to level 8 at Luci's magick shop in Port Kuudad without investing a single skill point.)

This impacts your natural rate of hit point recovery, and increases resistance to toxins and disease, but we never used it in our pacifist runs, just out of preference for other skills.

Combat Skills
There are lots of these for all different types of ranged and melee fighters, but we never used any of them on a pacifist run, since Eschalon Book II is winnable without having to inflict a single damage point on any foe. (Most of them can be trained from Sonya in Port Kuudad.)

Light Armor & Heavy Armor Skills
These will let you train to become proficient in types of armor, and so wear them without a penalty that will impact damage reduction.
This probably makes a big difference for players who battle their way through the game at close quarters, but we never needed them on our pacifist runs, since we spent our time evading foes, hiding, or casting nonlethal spells, and never noticed the penalties putting us at any kind of disadvantage.

Lets you use shields without a penalty, but we never used shields or the skill.

This skill can be useful since it will enable you to dodge attacks, and can cause an attacking foe to throw themselves off balance when they miss. (We never invested our own skill points in it, but it can be learned from either a skill manual, and possibly other special items to gain a few points. Even with just a few points, we noticed the skill being useful a few times when we got attacked.)

Optimizing Skills with Trainers & Skill Manuals: 
You will find many skill manuals that will cause you to gain several skill points from reading the books. If you read a manual about a skill you've never learned before, it will teach you the skill and grant you one point. If you read a manual after learning a skill, it will add at least one more point, maybe more. However, to optimize your gains, you should ideally not read the manual for any skill that you intend to train in later: If you hire an NPC to train you in a skill to the maximum trainable level 8, you can then read the manual afterward and gain additional skill points. (If you read the manual early you'll still gain the skill points, but it would grant you skill points you could have just bought for some gold instead.)

Also see the "Trainers" section for a list of all trainers found in Eschalon Book II.