Prospect no IMO. The exception is to prospect for Jaspers. You can turn them into some ring with a chance of a blue (rare) proc. Sell the blues and DE the rest. Then sell the DE mats (Hypnotic Dust and what not) on the AH. Of course you have to have an Enchanter also. With the remaining green gems from prospecting you can turn them into good blue gems with Alchemy and cut those gems into whatever gems are popular on your server. You can also use the purple and orange (green) gems to craft items, but they require 2 gems each per item whereas the Jasper takes only one. I usually ended up vendor a LOT of the blue, red and yellow gems of green quality.
Use an AH addon like Auctioneer. After a few weeks your software will tell you which gems sell the most and the best. Mainly it's the red gems, i.e. +STR, +AGI, +INT, etc. So there's a lot of competition for those, but they're purchased a lot too. Start there while you're researching the market.
You can use some part of the HB bot to make sure you have the lowest AH prices all the time, but I haven't looked into how, and I understand (from reading various forum posts) that excessive use of that AH bot feature is a good way to get banned. Again, I've never tried it. So take it with a grain of salt.
Making gold from JC (like Ench) can be VERY lucrative because every class needs JC for PVE and PVP. However, making gold from JC is not automated and takes a lot of research, analysis and time to prospect, vendor, cut the gems, post them on AH, get the ones that didn't sell from AH and re-post them on AH, etc. Maybe it's more time efficient to just sell the ore and uncut blue/purple gems on AH as is. Or just do Herbalism + Mining for gold, or dailies.
More specifics if you want. I've done a bit of research on JC, Ench and Alch, but most importantly, remember that everything I've just typed will be meaningless in 15 days when MoP comes out. Good luck!