Going to start a list. Thankfully, they tell you what the things do before you add them.
Colorless
(20 Quest)
+6 stat
(25 Quest + 5 Raid)
+1 Exceptional Stat
Yellow(30 Quest)
Spell Focus:School
Proof Against Poison
Blindness Immunity
Disease Immunity
Fear Immunity
Underwater Action
Featherfall
Resist 4
Protect 4
GFL
Wizardry 6
Red
(20 quest)
(adds this property to your weapon)
Adamantine
Silver
Cold Iron
Byeshk
Crystal(new type)
(30 Quest)
(adds this property to your weapon)
Good
Evil
Lawful
Chaotic
(15 Raid)
+7 enhancement
Blue
(30 Quest)
15% ASF
Toughness(20 hp, doesn't open enhancements, doesn't stack with Minos)
+2 luck(skill and save)
+2 max dex bonus
Heavy Fort
+4 Natural Armor
(15 Raid)
+7 Enhancement
edit: Oh wow, someone screwed up the Catalyst menus quite badly.