If you chose Hermosa for your trainer, you get to use a +5 Skills book, Kenneth requires you give it up.
If you choose Barbosa instead of Allan, you get to use a +5 Intelligence potion that Allan requires you give him, and I think you also get an extra skill book. Allan does let you make the best armor rating potion in the game, though.
If you choose Jo... Jo-someone over Igor for your necromancer, you get an extra skill book from his quest (it might be a bug, but it's in there unless it gets patched).