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Starting at level 3, each time you level up, you can make your weapon more powerful. If you're playing a character who actually uses his (or her) weapon, then it's best to pick bonuses that increase damage. Otherwise you should add useful properties, like healing spells.
Here are the bonuses you can add.
1 point of fire damage
2 points of cold damage
1d4 points of electric damage
1d6 points of acid damage
Something Special when Hit:
Confusion DC-26 25% / 3 rounds
Daze DC-14 25% / 3 rounds
Massive criticals 1d6 damage
Poison DC-14 1d2 constitution damage
Cure Light Wounds (5) / Cure Moderate Wounds (10) / Cure Critical Wounds (15)
Neutralize Poison (5) / Restoration (7)
Also, starting at level 12 (should you somehow get that high), every three levels you can ask for a general +1 weapon enchantment.