Fortunately for tanks no one will be using the Blue or Green gems. Reds are pretty much hands off since everyone other then tanks has a use for them. What ends up happening is that since the reds are in such high demand, people start requesting Purples and Oranges. Rogues will most likely soak up your first few Yellows, but eventually you will have a surplus of them.
You need to make sure that the pieces that people will want to socket will be those that they are planing to hold onto for a very long time.
The safest way to go about it is only hand out gems for T6 of equivalent gear till you get 10 or more of that color gem in the bank, then you can have a said class go to their CL and have him/her clear the piece that they want to socket. Red, Purple, and Orange gems should be on the restricted list of those gems that shouldn't be given out unless they intend on keeping that piece till Sunwell.
I would also setup some form of gem request system on the forums instead of handeling it through tells so that it can be tracked much better and there is more fairness to it so that someone who has been waiting for a gem for a week does not get cut in line by someone who just snaged an item.
My guild only permits the gems on Kael'Thas gear on up.
If there are a surplus of gems, they're available to the guild at a reduced rate. We still have a backlog of gems, despite having the first kill of illidan at the beginning of December. Crimson spinels are a hot commodity.
I just have a gem request / gems received forum thread. Anyone who gets PVE gear that they aren't going to replace, we just put a request up. We have a sliding cap where we try to ensure that everyone's received roughly the same number of gems. We try to make it clear what quantities of gems we have. As much as everyone wants spinels, they'll have to accept that we can't fulfill everyone's wish lists.
You can go off with merging them somehow into a seperate DKP list to track them all, but it seems like a lot of extra work. Just a minor system (list) to try to make sure that they're getting reasonably distributed is probably all you need.
My guild at first only gave out 1 gem for 2 socket items and 2 gems for 3 socket items (and 1 gem for 1 socket items), and only for stuff from Hyjal and Black Temple; raiders had to trash farm to get gems to cover any empty slots or get a heroic gem or just get a blue gem off the AH.
Now we do full comps on gems but we place limits on red/purple/orange, i.e. for a 2 or 3 socket item, if you want the guild bank to give you 3 gems for a 3 socket item, the 3rd gem must be yellow/blue/green; if you want 2 gems for a 2 socket item, one of them must be yellow/blue/green. Also we don't tend to comp offset items with gems, especially ones that are high in demand and low in stock.
Currently my guild's bank has like 50 green, 40 blue and 14 yellow (when we opened these 3 colors up to our members to buy for pvp, the yellows went pretty fast, and we just naturally have through "luck" a gratuitous amount of blue gems, even after we sold some).
Once Blizzard implements a resi/stam seaspray...woooooooo.
Anyway I think our stocks on purple/red/orange are like...single digits...or maybe in the teens lol, it's a combination of people wanting them and a low drop rate (for us).
We only handle gems for BT or Hyjal gear. When we started with Illidan we also got gems for those pieces of gear we are gonna have until Sunwell...
- We got some gems from Xmas, and on Illidan first kill. Those were FFA and we could even AH them.
- On farm runs for HoDs (we did them outside raid hours) we got all dropped items for free, so we got gems, epics and marks for our "obsolete" gear.
In summary, TBC raiding is easy. 9/10 encounters can be summarized with 1 phrase. Stay out of the fucking fire. Panda Cub with a Gnome pet!