I am fairly new and inexperienced at the JC market. So remember that when you read anything I say about it. These are the things I do with it. They may be a huge mistake or I could be on the right track. One of the first things I had to deal with was picking a new cut.
You first need to know what your goal is. Are these cuts for yourself/friends or to make gold? One does not rule out the other but you usually end up giving on something. If its for you or your friend the choice is easier. Just pick the cuts you use the most and off you go.
If you are looking to make gold, different things need to be looked at. I started by looking at the cut gems that listed for the most. The mark up is higher to the profit is greater. How many sellers are listed? The more sellers, the more competition. So for my first few gems, I also looked at how many sellers and gems each had listed.
Now rule out any that look questionable to you. Is it a gem that someone would want. If you see one Tense Eye of Zul (10 hit/13 spell pen) for 250G its probably not going to sell. Who would buy that? This could turn out to be a very profitable gem. I have no idea. But for my first few gems, I want something that feels a little more useful.
As you start to pick up more and more cuts, try to get a few of the other colors. If you focus in one color of cuts too much its possible you will drive the cost up on them (from buying so many to cut and re-list). You will be set up much better if you give yourself that flexibility. If you end up prospecting later, you will end up with gems of all colors.