I've got a 5dII on order and had also been wondering about sound.
I know I can plug in an external microphone, so that will sort out the in-camera sound quality.
However, there are several remaining problems.
1) I hate things dangling from the camera, including the strap. They easily get caught on things like the tripod and can be a liability. I can see working with a microphone deliberately placed away from the camera is going to be a real PITA.
2) I believe the 5D will not do sound-only recording; so I'll need to take movies just to capture sound for merging in when editing.
3) I've read the 5D wont allow audio annotations on images, which is a shame as I've used it successfully on some compact cameras. If the 5D did allow audio annotations then I guess it would also solve point 2!
To fix the above I'm currently looking at getting either a Pocketrak 2G or it's bigger brother the Pocketrak CS. They are very compact and reasonably priced; either of them ought to be plenty good enough for my needs.
There's an excellent review at http://www.musiciansfriend.com/document/ya...r?doc_id=103481