A common question I receive from emails is “What gems do you cut for profit?”
There are really two answers to this question, each has pros and cons.
First You can craft the commonly used gems. To get a good list on what cuts are used the most, check out WoW Popular. They give a nice list of the most popular gems being used across all servers. The Pro to this method is that you will sell gems quickly and in mass quantities. The Con is most Jewelcrafters will be doing the same thing, this makes undercutting pretty common.
One way to adjust for the undercutting is to list the gems for 12 hour auctions. This allows you to relist the auctions quickly if you are undercut and they do not sell. This also saves you some money from deposits.
The other method is to get unique cuts that have mid range demand. On my Server you can sell a Deadly Ametrine or Stark Ametrine for 50g + more than the more common cuts. The Pro is you make more money per gem. The cons are you will not sell as many and may have auctions expire.