Use ffmpeg as described in the Gentoo Linux Wiki.
nice ffmpeg -i movie.avi -acodec libfaac -ab 128kb -ac 2 -ar 48000 -vcodec libx264 -level 21 -b 640kb -coder 1 -f psp -flags +loop -trellis 2 -partitions +parti4x4+parti8x8+partp4x4+partp8x8+partb8x8 -g 250 -s 480x272 movie.mp4
\windows\system32) using 7-Zip
Convert any movie using:
start /low ffmpeg -i movie.avi -f psp -r 29 -b 768k -ar 24000 -ab 64k -s 320x240 movie.mp4
Note that the conversion is done at idle process priority, which should always be preferrable. Your system will be fully usable during the conversion, but it will not run slower if you do not use your system during the conversion.
Don't be afraid to run several conversions at once. Given reasonable HD buffers, they will not interfere, and may actually run faster than converting them one at a time.