Oh man those are gorgeous

I've changed a few so not all are needed, but definitely using what I like of what you have there, thank you!
New Changes:
Changes:
Swapped from hooks to overload and standardized gem effect for the base set of gems.
Changed weight to hopefully play nicer with other addons.
Color changes:
Agate is now Blue
Ametrine is now Violet
Spinel is now Red
Topaz is now Yellow
Opal is now White
Diamond is now White
Fire Opal is now Yellow
Pearl is now Blue
Bloodstone is now Green
Tier Changes:
Quartz moved to T1
Zircon moved to T2
Opal moved to T3
Moonstone moved to T4
Jade moved to T5
New/Removed Gems:
Chrysocolla removed, T1 Blue
Nuummite added, T1 Black
Verdite added, T1 Green
Jasper removed, T1 Black
Tiny Geode added, T1 Stone
Small Geode added, T2 Stone
Geode added, T3 Stone
Large Geode added, T4 Stone
Enormous Geode added, T5 Stone
New Icons!
Standardized base gem color with gem effect:
Black is now Stun Resist on Wear/Imbue, Lifetap 2%/tier on bomb.
Blue is All Stats on Wear/Imbue, increased Bomb damage percent.
Green is Defense and Saves on Wear/Imbue, +5/tier Mana Burn Splash for bomb.
Red is +1%/tier Spell/Mind/Combat Speed and -1%/tier Spell Cooldowns on Wear/Imbue, +5/tier Fireburn Splash for bomb.
Violet is 2% Crit Mult and 2% All Resist Pen/tier on Wear/Imbue, Mana regain on bomb (10/20/30, 30+10 arcane splash, 30+20 arcane splash, to keep from basically getting a ton of mana per bomb toss.)
White is All Resists/Armor on Wear/Imbue, Daze with later stun on bomb. (T1: 20% daze 3 duration; T2: 40% daze 3 duration; T3: 5% stun 2 duration; T4: 10% stun 2 duration; T5: 20% stun 3 duration)
Yellow is +all Damage/Crit on Wear/Imbue, +5/tier Spellknockback splash on bomb.
Stone (new) is +1HP/mana/Stam regen/tier and healing 1%/tier on Wear/Imbue, negative 2%/tier bomb damage and 10 poison damage splash/Tier on bomb.
Stone is its own category for now, and I'll probably introduce an anti-magic artifact one of these days for the category. I was going to go green, but I'd rather have a new category for consistency's sake of one common gem per. I'm not quite sure I like it or not.
Checking the runic-golem add on, it will declare anything not of the default seven colors as multi-hued, which I'm fine by, it's more of a natural element than anything else. This works for now, I do not expect minmay to cater to any new categories I may add, but I will keep that interaction in mind, even if it only does affect one class.
I've toyed also with the idea of mixing about on rarity for some possible new options of gems, but I've decided against it, as the Extract Gems talent of the Stone Alchemy tree doesn't seem to take rarity into account, so they'd be nearly just as common as everything else for them.
We end up Losing the following:
Worn Effects:
+1 Light Radius, +2 Infravision
+10 See Invisible
Bomb Powers:
Bomb Thrown Range
+Lite Damage Splash
+Poison Damage Splash
+Slow damage Splash
+Ice damage Splash
+Acid Damage Splash
+Fire Damage Splash
Please note, I am not a geologist, any accuracy is to be considered thrown out the window. Please do not try to channel gems at your friends or family, they may look at you as if you were odder than you already are. Thank you SO very much to rexorcorum for the icons!
I do agree with HousePet and Hachem_Muche that right now it is quite cookie cutter, but I do want to add more in the future, though I do not want too many in the game, for fear of over-saturation due to their low rarity. Possibly some anti-magic stones/artifacts, who knows. But for now, I nailed down some sort of consistent scale to work from.
Any comments on how over/under powered some new gems would be great too, but if something it's OMG BEST IN CLASS, that's fine, not every gem will be for every character build.