I previously posted all of this information in a thread at the Ubuntu forums, but I wanted to post it here, too, so I could update it as new versions/information arise. This is a list of all of the GUIs/frontends (that I know of) for HandBrake, along with information regarding features/limitations and development progress for each.
1. GHB is the official GTK GUI that is included with the HandBrake source code (currently just available in the SVN repository). It was written by a swell guy known as JohnAStebbins from the HandBrake forums and it's nearly on par with the OS X GUI in features. However, some people have trouble getting it to compile. On Ubuntu, it requires at least Hardy. (you can download 32-bit and 64-bit deb binaries from here or you can compile from source using HandBrake's official SVN repository [directions here]).
2. qtHB (aka qHandBrake) is an early, yet promising GUI based on the official QT4 HandBrake code that languished in SVN until a HandBrake forums user known as gonza updated it recently. It is still in early development and not yet included in the official SVN code, but it is nearly as complete as GHB and significantly easier to compile (fewer dependencies). (You can read about it here or download and compile it using my instructions here).
3. HandBrakeGTK (aka RippedWire) is a port of a Windows CLI wrapper that requires mono-devel to run. It has a bug that causes it to not pass advanced x264 options to the CLI, which is a total deal-breaker for me. However, its queue feature works well, so it can be useful for batch rips if you don't mind using baseline AVC. It also works well with other codecs, such as xvid, that don't suffer from the adv. x264 opts bug. Another advantage is that you can easily update the HandBrakeCLI backend without affecting the graphical frontend. RippedWire does not appear to be in active development. (read about its history here or download it here. 64-bit users can try this one, which I built from the author's mono project files on my 64-bit system [just install mono-devel, move the executable into the same directory as your HandBrakeCLI binary and type mono HandBrakeGTK.exe]).
4. gHandBrake is a GTK CLI wrapper written from scratch by a guy that goes by Derrik81787. I later added x264 options to it, but I'm a terrible programmer and it ended up really unstable. Derrik seems to have dropped the project because his site for it is gone (Update: he's too busy with classes to work on it now but plans to revisit development in the future), but I would love to see someone tweak the code for better stability (the big issue appears to be with malloc, which I know nothing about; leave a comment if you'd like to pitch in). The major advantage to this frontend is that it is really easy to compile and it has very simple dependencies, unlike the official GTK GUI. (read about it here or download it here).
If you have anything to add, or if you have any corrections, please leave me a comment.