wierd, i came here to ask the same question. I'm in need for creating a wmv, i usualy do quicktime, but for one reason or another i need a wmv. is there anyway to do it out of FCP? or a free progarm to use?
Seriously, though, WMV is a better format than Quicktime, IMHO, having nothing to do with any Mac/PC rivalry. The quality to file size ratio alone knocks QT out of the park, to say nothing of its ability to encode things like 5.1 surround.
QT may catch up if it implements H.264, but for right now, I definitely seriously consider WM9 the superior format.
Fortunately, H.264 is one of the codecs that's highly touted in the next major Mac OS X release. I'm definitely looking forward to its arrival.
As far as QuickTime goes, though, I have to stress that it's a media file format and not a codec. (For that matter, there are a variety of WMV codecs as well.)
For video, QuickTime's MPEG4 isn't significantly different from, say, XviD ISO MPEG4 or Windows Media's own MPEG4 and MPEG4-derivative codecs. These are all very high quality codecs, and H.264 looks to be noticeably superior still.
For audio, I don't think 5.1 channels is a good idea for the web, but QuickTime AAC definitely supports this (up to 64, technically).
In the end, I think comes down to preference ... it's hard for me to choose for purely technical reasons, because there are excellent options on both sides. 8)
Oh, and sorry to stray off topic, but you might want to try Cleaner for the Mac; it can turn out WMVs. Otherwise, if you have a PC handy, you could try one of the tools available there if you output to an intermediate file.
You could always export it as an uncompressed quicktime and then get a friend to compress it in wmv from his PC. Other than that, Apple doesn't seem to likely to support that format anytime in the forseable future.