HandBrake is no longer limited to DVDs: it will now accept practically any type of video as a source. This massive enhancement was achieved by tapping into the power of libavcodec and libavformat from the FFmpeg project.
There is now an official GTK graphical interface for Linux, available as a binary for Ubuntu. This is the real deal, interacting directly with HandBrake's core library instead of just putting a pretty face on a command line interface. It has full feature parity with the Mac interface.
The x264 project has really come into its own this year, and HandBrake 0.9.3 integrates the latest improvements to the H.264 encoding library. Picture quality has enhanced dramatically through the use of psychovisual rate distortion and adaptive quantization, and there have been significant speed optimizations.