Amanna over at the Adventures in Azeroth blog has put together a useful "gem research center" for finding gems to fill those slots. Basically, she's just created some filters on Wowhead for you, so that if you need to find all the purple gems, all the Epic rated gems, or even something as specific as all of the Resto epic gems, the info's just a click away.
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.