CORE

- AC3 in MP4 support
- Multi-track audio support for Apple devices
- Better handling of audio discontinuities
- More flexible, "loose" anamorphic
- Variable frame rate encoding
- MP4 optimization for progressive downloads
- Dynamic range compression for encoding from AC3 audio
- Ability to encode an audio stream and pass it through at the same time
- iPhone-compatible anamorphic (pasp atom)
- Robust program and transport stream support
- Better handling of DVD read errors from invalid VOB units
- Detects and works around missing end of cell markers
- Recovers from loss of signal in a stream
- Drops subtitles less often
- Keeps chapter markers in better sync and prevents duplicates
- Better handling of B-Frames
- Tunes FIFO sizes by CPU count
- Finally squashes the bug that cut off the end of movies
- Preset changes
- Standardizes on standard out for progress and standard error for everything else.
- Correct channel counts when passing AC3 audio to Matroska
- Tag MP4 files as encoded with HandBrake
- No more merging short chapters
- Newer copies of x264,
- VBV 2-pass patch for x264
- Sets keyframes for x264 by frame rate.
- Support for >2GB MKV files in Linux
- Code audio languages in a way QuickTime understands
- Better subtitle positioning
- Fewer crashes in 2-pass encoding

MAC

- Leopard Only
- Sparkle
- Reads .eyetv files as well as .dvdmedia files
- Much better queue
- More white space
- Code restructuring
- Activity window logging, complete with a "black box recorder" for crashes
- Ability to open a single title for a DVD instead of scanning the whole thing
- Warns people when they try to queue up two files with the same name
- Maintains picture filter states between jobs
- .xib Interface Builder files SVN can track
- Switches to NSImageView for previews, so no more useless OpenGL effects
- Temporary loss of localizations for foreign languages (the old system was broken anyway)
- Separate filter settings for every queued job

WIN

- Query Parser
- Sparkle-compatible update checker
- Activity log window
- CLI built-in preset parsing
- No more admin rights required in Vista
- Handles more display resolutions

CLI

- Built-in presets
- Short names for denoising (weak, medium, strong) and deinterlacing (fast, slow, slower) 
- Solaris port
- No more x264b30 (use -e x264 -I -x level=30:cabac=0 instead or better yet an iPod preset)
- Chapter marker .csv input fixed
- CRF as default quality mode for x264, now -q is CRF and if you want CQP add -Q to it