Handbrake 0.9.9 supports pushing video cropping and down-scaling operations to the graphics processor via OpenCL, thanks to work done by AMD. They also contributed a Windows-only DXVA video decode acceleration patch too. On the Intel side, there is now Quick Sync Video support for accelerating video operations. Quick Sync Video though is a Windows-only driver feature where on the Linux side their crew only exposes the video calls over VA-API.
Some other changes to find with Handbrake 0.9.9 include Blu-ray PGS sub-title support, support for new video frame-rates, better audio remixing support, updated libraries, and various other bug-fixes and improvements.
More details on Handbrake 0.9.9 can be gathered from the release announcement and the 0.9.9 notes.