So why use trepanning in your game? Perhaps a player character has developed a mental illness or psychosis and this is the recommended treatment for his/her society. Perhaps trepanning is a rite of passage for a group of clerics or shamans, and the trepanning bestows special powers. Perhaps it is done against their will. I am sure that clever GMs will find a way to work this into any campaign.
Trepanning Random Effect Table
Roll a d12. (optional) +1 if the trepanning is done by someone with training.
1 - Oops! Character dies
2 - Ouch! Lose 1d4 HP
3 - Ugh! Lose 1d4 Wisdom
4 - Whoops! Lose 1d4 Intelligence
5 - Uh Oh! Loss 1d4 Charisma
6 - Oh Man! Loss 1d4 Constitution
7 - Eh. No effect
8 - Not bad! Gain 1d4 Intelligence
9 - Good job! Gain 1d4 Wisdom
10 - Release the spirits! Gain one psionic power
11 - The Gods talk to me! Gain two psionic powers
12 - I can see the universe! Gain the ability to cast 1d4+1 cleric spells at will. Pick spells at random.
13 - I am Lord Azrael! Character becomes possessed by demon or celestial being. Grant powers and weaknesses from Manual of Monsters.
Note: If psionic powers do not exist in the game world, then grant the ability to cast a cleric spell at will.