My 30D works fine in Av mode with manual focus lenses; I'd be surprised if the 60D didn't but I don't have a reference handy to back that up. On my 30D the LCD reads "0.0" for the aperture when it can't communicate with the lens.
My camera meters in Av mode without any problems (though some of my manual focus lenses expose differently by half a stop or a full stop at different apertures (I'm not sure why), but they do it consistently, so it's just a matter of learning the lens or chimping for exposure and setting exposure compensation to correct for it).
I just tested, and exposure bracketing works correctly in Av mode.
I can't answer the flash question.
If you haven't already seen it, there is a good site on manual focus lenses on Canon DSLRS here: http://www.bobatkins.com/photography/eosfaq/manual_focus_EOS.html
As far as limitations:
- you can't use Tv mode, P mode, or any Auto mode (anything where the camera will try to set the aperture), of course
- you're most likely looking at lenses without Auto Focus or Image Stabilization.
- you'll lose the aperture Exif field, so if you want to know later what aperture you used for a picture, you need to either take good notes or infer the aperture from other clues in the picture (shutter speed, how much light there was, etc.).
- If you're looking to buy manual focus lenses for a cheap way to get a fast lens, realize you won't be able to see the actual DOF beyond about f/2.8 through the viewfinder (also true of modern lenses). I've heard that Live View shows the actual DOF.
- If you're looking to buy manual focus lenses for a cheap way to get a sharp lens, realize that older lenses don't have modern coatings and are often outperformed by newer, cheaper lenses.
- If you're going to focus at the widest aperture for the most-accurate focus then stop down to take the picture, you have to (of course) physically move the aperture ring. For just taking pictures while wandering around that's not a big deal, but for fast-moving subjects (like birds) it can be a little difficult; for macro work it can be a major pain.
Make sure you choose a lens (mount) that doesn't require optics to focus to infinity, or you'll just end up disappointed with the image quality.