Well, this is kind of a massive list, but I think this is every class skill that I either would never practice, or have...and never found a use for. Some of these are borderline marginal, but figured I'd mention them.

General - Pen. For the love of....can't this just be generic?

Berserker - Take Cover
Berserker - Overrun

I've had both of these skills, and I have only seen take cover work ONCE over multiple Skruggas. Overrun I've never managed to make work.

Conjurer - Armor

Druid - Tsunami
Invoker - Create Water vs. Create Spring
Invoker - Drown
Invoker - Tsunami

I'll mention these all together. First 20 levels of water path are making water ungodly repeatedly, and do they really need to be able to both make it into a container, and as a spring?

Then finally you can do damage, but it's on/in-water only, and 98% of the things you find there are immune. I'll admit in theory they have a use, but in practice I never found it. As an aside...invokers also have no way to innately go underwater until level 38, which is sort of ironic. Air Path spell "Air Bubble"?

Necromancer - Speak with Dead
This one I literally don't remember what it actually does that accomplishes anything, aside from the Tribunal necromancer.

Paladin - Ceremonial Burial
Paladin - Revelation
Ceremonial Burial is just so specific, you never get to use it. Yay for stopping the one random necromancer around from animating it or using gravesight. Revelation I've tried to use, but finding out if someone's standing *right* next to you tends to end up being useless unless you have that area attack, and then I pretty much use the area attack at random. I'll admit it's another theoretically useful spell.

Ranger - Plainsrunning
Ranger - Bramble Pit
Ranger - Poison Arrow
Ranger - Flaming Arrow
Ranger - Aerial Shot
Ranger - Precision

Plainsrunning. OMG, a once per hour run five steps in a straight line? It was useless.
Bramble pit's borderline. Before they know better, sure. After they know you have it? Easily avoided. Also, who doesn't run around with boots on?
Poison/Flaming arrow. Waste your active command choice to attempt to change weapon damage, which attempts to land like normal, and attempts to land poison/immolation. I'd rather just grab a poisonous bow. Even if these would dip the weapon *AND* fire it for an extra shot like backhand, it'd be useful.
Precision...I'm probably going to practice with every character because it sounds useful, but I've never figured out exactly what it accomplished.

Thief - Appraise
Thief - Shadow Drag
Thief - Grapple
Thief - Disengage vs. Shadow Disappear
Thief - Isolate vs. Separate
Thief - Discerning Gaze

Appraise - How is this significantly more useful than lore? Especially if I can get it with observation experience instead of thief points.
Shadow Drag - Oh...shadow drag, how I hate thee. Amazing in concept. In practice, everyone just keeps trying to yell "help" or uses "vis" to negate it.
Grapple - Why it over disarm?
Disengage vs. Shadow Disappear - Admittedly there's a huge level difference, but if I could wait to get a skill that gets me out of combat *and* instantly hides me? Deal.
Isolate vs. Separate - These are so oddly similar, yet different. Remove enemy from room, one starts combat, other doesn't. One tries to disarm if you're barehanded. Do either get used anyways?
Discerning Gaze - Don't you not receive an echo for looking at people if the thief is not visible to the person, or sneaking? I swear I never notice thieves looking at people anyways.

Warrior - Hook

Especially now that broken weapons remain, I'm pretty certain I've never bothered to hook a weapon in my life. Yes, I can hook whips for probably better success, but if I'm not weaponbreaking, I'll probably settle with disarm.