For awhile I was enticed by several things about Badaboom and Media Espresso. Badaboom did really fast encodes and only the GPU was used, the CPU was free for other things like full speed web browsing. Eventually I gave up though because the resulting files didn't look anywhere near as good as Handbrake renders. Yeah, Handbrake took a lot longer and tied up the computer during this time, but in the end the final quality is what really matters.
No one has gotten GPU h.264 encoding right yet. I had been using Handbrake but have recently switched over to MediaCoder because it will read and write virtually any format video and audio, including Cineform, and it has a three-pass mode which is really good at keeping the bitrate constrained to the minimum, average and maximum values that I set. It isn't for the faint-of-heart though, there are a lot of available settings and one must know what they're doing.