I'm very biased against Quicktime, for the reasons KDR has already mentioned. It works, but I just hate the player and the format and everything. For instance, if you embed the Quicktime file in a web page, it's almost impossible to permanently download the file to watch later. The player doesn't include a "Save Target As" type of function. It drives me nuts looking through Temporary Internet Files and/or the page source code to try to find the actual file for later viewing.
Windows Media is actually very efficient in terms of file size, but I'm well aware of its compatibility issues. MPEG is way too big for us to use; anyone on dialup would be left completely in the cold.
We host movies in the format we receive them, which is why some movies are Quicktime, others are WMV, etc. But whenever I'm encoding movies myself for PGC, I use DivX. So far I have not messed with audio compression, but now that I'm feeling pretty confident with the video setup, I'll look into it. This is all very new for me; I knew jack about video editing two weeks ago, so I feel like I'm doing pretty well so far.