I've been recently using mencoder form
http://babgvant.com/forums/ShowThread.aspx?PostID=3815
It's a one pass / mp3 audio profile (that I slapped together without much knowledge of what works best to give the best quality. )
I use the command line: mencoder.exe [input] -profile X264-MP3-HQ -o [output]
where the profile (in the Mencoder.conf file) is:
[X264-MP3-HQ]
profile-desc="H.264/MP3 Good Quality"
lavdopts=threads=2
vf=pp=md,crop=704:560:4:8,scale=640:352,harddup
ovc=x264=yes
x264encopts=crf=23:subq=6: partitions=all:8x8dct:me=umh:frameref=5:bframes=3: b_pyramid:weight_b:threads=2
ffourcc=H264
oac=mp3lame=yes
lameopts=fast=yes: preset=medium
#DtbExtension=avi
Note: The space in [subq=6: partitions] is not really there - it gave me a smily and I couldn't quickly remove it so I put the sapce in.
Same for [yes: preset]
Don't know if it will matter though...