Update (5/15/09): I have working binaries of the latest code available in my PPA repository. Directions for adding it to your package manager are available here.
install git if you don't already have it (sudo aptitude install git-core), along with the dependencies for HandBrakeCLI, then type
git clone git://repo.or.cz/HandBrake.gitnavigate to the newly created HandBrake directory:
git checkout --track -b bonne/qhandbrake origin/bonne/qhandbrake
qmake && make
Unfortunately, qtHB *refuses* to bundle into a proper deb binary, but I believe you can download and run my precompiled binaries as long as you have the proper qt4 dependencies installed.
Download 64-bit qtHB
Download 32-bit qtHB