I use the rather tempremental cinelerra-cv for my video editing.
cinelerra-cv has problems with many video containers, but apparently less so with mov.

I also wanted to de interlace and scale the video for youTube.
The following command takes a video and does the above:

mencoder -ovc lavc -oac lavc -of lavf -lavcopts vcodec=mpeg4:vrc_buf_size=1835:vrc_maxrate=10000:vbitrate=8000:vqmin=1:keyint=25:aspect=16/9:abitrate=224:acodec=mp2:vstrict=0:dc=10:trell:mbd=2:precmp=2:subcmp=2:cmp=2:dia=-10:predia=-10:cbp -lavfopts format=mov -vf yadif,hqdn3d,harddup,scale=1280:720 -ofps 25 -o output.mov input.mpg

I got most of the command from:
http://www.coswellproductions.com/wordpress/2007/05/16/more-cinelerra-and-mencoder-fun/