Speed Conversion: Is Handbrake the best of a bad situation?

Hello All.
To cut a long-story short, is there a better way in which to convert video files (mostly AVI & MKV) to MP4 than using the presets in the Handbrake program? I have been plagued to optimise my video content for Apple TV2 and as such I have around 400 movies to convert so as to add them to iTunes for playback on ATV2.
Being a rookie to this sort of thing, I can’t help but hope there is a faster solution to converting file formats as I don’t fancy leaving my computer on for days (weeks even) just so as I can use ATV2 to watch my content.
Any advice would be greatly appreciated.
(If the advice is forget the ATV, I appreciate that too… it was a spontaneous purchase that has done little more than infuriate me).
Mikey
Answer #1
Jailbreak the AppleTV2 and install XBMC, or sell the AppleTV2 and buy a player which doesn’t suck out of the box (e.g. WDTV Live 2). Both of those options would allow you to play any content without having to convert it to MP4 (excluding 1080p mkv on the ATV2, the WDTV Live 2 will play 1080p fine).
http://wiki.xbmc.org/index.php?title=HOW-TO:Install_XBMC_on_Apple_TV_2
Answer #2
No idea what you are talking about…
Generally i highly recommend Total Video Converter. I tried many many programs and this one was by far the best.