At least level 1 for
Alchemy is useful for mixing
restoration potions, though you can get a level as a quest reward.
Repair level 1 is very handy (you may not always have easy access to a merchant or blacksmith). I am cheap, so put 2 skill points into it, and kept 3 items with a Repair bonus, to batch repair loot before selling.
Lockpick / Identify: I maxed both, though you can get a level or two for each as quest rewards. There are a couple chests/hatches that need Lockpick level 5, and I'd much rather have everything identified as I find it than bringing stuff back to a merchant.
Free skills, and spell books you can buy (spoilers)
