I have been using some alternate lenses (Contax and screw mount) on 50d, 40d, and XSI, but I have a 5D mk II arriving soon. I know there were some problems with the 5D mk I and mirror clearance with some lenses, and I found this chart which lists many Contax lenses being questionable for use with the mk I:
http://www.pebbleplace.com/Personal/Contax_db.html
Does anyone know if this problem also exists with the 5d mk II? In particular I am concerned about my Contax 28 2.8, which I like using very much. If I try an alt lens on my new camera and the mirror hits, could I damage the mirror or the camera?

This thread http://www.fredmiranda.com/forum/topic/718410 says the Rokkor 58 has mirror-clearance problems.

The chart in your link says there is no problem with the CZ C/Y 35-70 f/3.4 on a 5D. But a poster in the other thread reported a problem. I suspect that due to tolerance differences and sample variation on the 5D, we won't be able to know categorically. Experimentation with individual lenses on individual camera bodies may be the only way.