I am a fan of FFMPEG for most audio/video conversions, but when on windows, I cannot *easily* do the DIY scripting I can on Linux. WinFF is a GUI program for Windows/*NIX that neatly wraps around FFMPEG. Two really good things about it:

• huge number of presets for almost any video conversion (in my case H264 for web)
• spits out the ffmpeg command line options to show you what is about to happen, and lets you edit them!

be sure to use -threads 8 to keep your machine busy. Free of course, as it uses FFMPEG.