Since I didn't see this information elsewhere I thought I'd start compiling it here. I dislike replaying games I finish tho so I probably won't be doing a 2nd, 3rd, 4th, etc playthrough. I'll list all of the gems I saw and if others can provide me with screenshots (or savefiles) containing gems they found and which are not on this list I'll update it to include those as well.

Boulder Opal - Increase duration of all Earth spells by 3 seconds (Requires: Earth Class)
Furious Red Crystal +20% Primary Projectile Damage
Onyx Stone - Auto-collect nearby loot. Auto-drink Venom Elixirs, and Mana & Healing Potions when levels drop below 10
Pearl of Perfection +50% Mana Recovery Speed, +50 Armor (Requires Base 6 Intelligence)

Falen's Tear +15% Max Health, +20% Max Mana, +15 Armor, Limited Fire Protection
Karon's Tear +10% Max Health, +15% Max Mana, +10 Armor
Talisman Peridot +20% Damage to all Earth Spells, +15% Max Mana, +20 Armor (Requires Base 5 Constitution)

Cut Amethyst +15% Max Mana Capacity (Requires Base 4 Intelligence)