I've been using Capture One to process my X-Trans files more and more lately. I had posted some initial findings before about this, and since then, Capture One has pretty much become my standard application for processing files from my X-E1. I'm really happy with how the software performs, and it does a really good job with Fuji's files. Not only does it produce nice and sharp artifact free images, but the colour is really great too, even without having to do anything.
While Photo Ninja and Iridient Developer (especially since version 3) each have their own advantages when it comes to x-trans processing, I'm finding that Capture One offers the best all round set of features. Because it's a much bigger application, you can pretty much do everything you need to in it without having to go to another application. It's shadow and highlight recovery are excellent, and it has a nice layer system for making local adjustments, and it has some really great colour manipulation tools, especially since the latest 8.2. In 8.2 they added a three way colour corrector which is similar to what is found on video and film grading systems (and was also in Aperture) which allows you to control the colour balance of the shadows, mid-tones and highlights separately.