This is a list of skills that either need non-linear balancing aka they don't scale, or they have some other issues that I was able to pick up on:
Pure offensive skills
Shatter - needs nerfing. At least until people get used to using other skills
Bolt of Gloom
Bone Shatter - the status effect is linear
Shield Skills - Most of the shields have a linearly growing amount of HP which doesn't keep up at all with the monster damage
(EDIT: actually I checked again and that's not quite true. Only 1 or 2 have HP. Some others are still not good choices though.)
Shield of fire - reflects back percent damage and raises resistance. Probably needs to go higher to be worthwhile.
Ice Armor - adds to armor linearly
Energy Shield - reflects back percent damage and raises defense. Looks pretty good actually.
Disarm Trap - I've seen it reported (in the DoP thread) that this doesn't scale well.
Poison Arrow - the Poison Arrow status is linear
Bark Skin - armor boost is linear and insignificant in later levels
Blight - already non-linear. Just need to check that it's enough.
Breech - has an armor component that's linear.
Inferno - already non-linear. Just need to check that it's enough.
Blood Sacrifice - may need to reduce self damage non-linearly because HP IS linear.
Gut - already non-linear. Just check it's enough.
Marked For Death - armor component is linear.
Curse of Pain
Block - I've seen it said that this needs a cooldown time of 5-10.
Summons - these will take me a while to calculate, because while they get a much lower level than you over time, they also get buffs.
Raise Dead - The only truly powerful pet spell. Pick a pet of any level.
LightningWard - are the wards useful at all? The stats seem very disappointing, but I've never tried them.
Circle of Protection - are these useful?
Circle of Power
Earth - not much use. Earthquake is the only affected offense spell. Crisses suggested that it should enhance poison as well.
Demon? - I can only tell after I do the math for summons.
Did I miss anything?