MOV is a video container (like AVI) but it doesn't say much about what is in it. It's like saying, "I really like that stuff I ate out of that white paper box in the fridge" -- probably not a hamburger, but who knows?
From their website it appears that the Canon 5D Mark II encodes its video as H.264 in the MOV file. H.264 is a highly compressed delivery format, not an editing format. The content of any given frame often depends on the frames that came before or even after; that's why it is slower.
You can lose no quality by converting to lossless compression -- the picture is already compressed, but won't get any worse. The file ends up much bigger (although not as big as uncompressed), but with modern CPUs and drives, you might be able to play HD in realtime without stuttering. (The trade-off is: if there is little or no compression, the amount of data is huge, and may not come off the drive fast enough; but if too compressed, the CPU may not be able to decode fast enough.) Try doing 30 seconds.
In the old days, I would have suggested Huffyuv on Windows, but nowadays try Lagarith.
Once you are done editing, if you want to share it, you will want to encode it into a delivery format like H.264. In addition to the file being smaller, people are more likely to have it already installed on their system.
the white paper box in my fridge is either pizza or leftover chinese. (depends on the size of the box, really.) +1, nice writeup. – quack quixote – 2010-03-25T08:31:59.707
I was going to mention the "wire handle" but the sentence was long enough already. – Ken – 2010-03-25T20:47:56.613