MediaCoderHq - The best encoder/program I've used. I've tried FFMPEG+VirtualDub among other combinations and this one just spits out the results in minimal time. Downside is that the website and UI is very unfriendly and takes some time to setup, after that though you can encode pretty much any format/codec you need. I have never had a video/audio-sync issue nor file format incompatibility with the program.
It's free by the way.