I've been using RawTherapee and ViewNX mostly, and I've recently tried Capture NX-D. So fare my favorite is RawTherapee, although I still have some issues with it. I'll list some pros and cons of the tools, based on my experience and some things that I've read here and there.
ViewNX is the simplest of the three, mainly due to the limited number of possible adjustments. Its main issue in my opinion is the lack of a noise reduction and curves tool. Some adjustments, like desaturation, require the creation of a Picture Control profile and are therefore cumbersome.
Capture NX-D is much more complete, but every time I try to use it I get annoyed by the GUI. The settings are not easy to spot, buried in a tiny portion of the window, and there seem not to be shortcuts to access them.
RawTherapee has tons of different tools and adjustments, conveniently arranged in tabs. It has tonemapping, light/shadows pushing and pulling, B/W conversion and several noise reduction tools. I find the noise reduction a bit light, and the sharpening a bit too subtle (it can do little with bad focus for instance), but perhaps there's a good reason for it.
Both Nikon tools alter the RAW files when adjustments are made, although they can somehow be restored. RawTherapee, on the other hand, creates separate metadata files that store the changes, keeping the RAW files intact.
RawTherapee uses a processing queue to convert the files, according to the adjustments that have been set. Capture NX-D and ViewNX require you to select the files to convert after having made the adjustments. I find RawTherapee's approach more convenient, as I can put the pictures in the queue right after I've applied the adjustments.
I had stability issues with RawTherapee, which tends to crash when the ram gets full (I have 6 GB). This happens when browsing large folders, or processing somewhat large images. Sometimes this gets quite frustrating; fortunately the changes don't get lost, because of the meta-files. Also the processing queue is kept.