A listing of all the free skill points you can get during the game. Not inclusive at this time, I'll add to it as I find more. Heavy spoilers ahead.....
Restoration - if you manage to cure both soldiers in Aleroth (you can create a second healing gem) Gomoe will teach it.
Restoration - if you find George's killer and report it to Mardaneus, he'll teach you a point.
Restoration - if you answer the statue's questions in Necorion's garden correctly, you'll earn a point.
Bless - if you rescue the child from the vampire and kill the vampire, when you stumble on Sir Markham on the road to Verdistis he'll teach you a point.
Trader's Tongue - buy all the items El'Gammon in the Blue Boar is selling. Test each one (simply click on them in your inventory) to enable the next set of dialogue. After about five items, he'll teach you the skill.
Identify - Complete the missing goods and broken wheel quests for Marcus the -complete- way (exposing black market and assassins, locating cache of stolen goods) and he'll teach you the skill.
Boomerang - Join the warrior's guild in the dark forest.
Note that it's fairly common to find spellbooks of specific spells throughout the game (both as loot and for sale); clicking on one in your inventory gives you one point in that spell skill. Nearly all are randomized, but one that seems to stay constant is Wizard's Eye, in a chest next to the Engineer at the bottom of the abbey.
The free skill points spoiler thread
Pickpocket OR lockpick OR evade traps - do both of the quests to join the thieves guild and Rob will let you pick which skill you want to increase as a reward.
Lockpick - in the thieves guild, accept the lockpicking challenge bet from one of the members. If you have a lockpick skill of 4, you'll be able to pick the first four locks but not the fifth. Report back to the thief, forfeit the wager (5000 coins) and he'll teach you a point of the skill.
Lockpick - in the thieves guild, accept the lockpicking challenge bet from one of the members. If you have a lockpick skill of 4, you'll be able to pick the first four locks but not the fifth. Report back to the thief, forfeit the wager (5000 coins) and he'll teach you a point of the skill.