Don't forget as well that gems aren't necessarily permanent-- while putting a gem in a slot uses that gem up for good, you can still place another, better gem in that same slot. So since this guide is here, now might be a good time to go back and look at gear you picked up and slotted a while ago, and see if there are any easy upgrades to find now. Amanna also has a list of BoP gems, so even if you're not a JC or don't have one available, there are places you can go to get your own shiny rocks.
Definitely worth a bookmark. Amanna is also planning on putting something like this (a list of Wowhead filters, I believe) together for gear, so we'll keep an eye out for that as well.