I had some video files sitting around that I wanted to convert to a format that I could use with the Apple TV (Second Generation). I tried dumping them into Handbrake on the Mac, which usually does an excellent job of converting, but it crashed every time.
I tried the same in the Windows version but it also crashed
As far as I could tell these files were encoded with XVID. I’m not 100% certain but that appeared to be the issue.
To get around this problem I ended up using ffmpegx. In my case, it worked perfectly. I used it to convert the XVID encoded avi files to H.264. I was then able to watch them via the Apple TV.