Basic editing can be done with freeware avidemux (
http://avidemux.org). Works fast, allows to trim beginning/end of the clip, allows to apply some filters to the picture, and you can remove audio with it. You can also convert formats and resize your video with avidemix.
It is not a tool for full-scale NLE when you have multiple scenes with transitions between, but it's a handy utility for quick basic edit of separate clips.
(I used to use VirtualDub in the past for that kind of work, but VirtualDub can't open MOV files from 5D Mk II, so I found avidemux instead).
P.S. Just found a forum devoted to video production with 5D Mk II:
http://cinema5d.com/P.P.S. Although Canon doesn't provide manual controls in video mode there is a workaround to force one of 4 aperture values (22, 16, 5.6, 2/full open)