With the changes from the patch merging the AH, you can make a killing off transmuting gems. Of course this will depend on your server but its working great on mine.
Golden Lotus goes for about 20g on average for my server and roguestones are going for around 8g a piece. The most popular gem right now is the Accurate Imperial Amethyst. . The average sale for an AIA is 120g currently. All you have to do is xmute the Imperial Amethyst and cut away. I can barely keep enough stock up on the AH!