I'm currently setting up a large scale (30k+ file) conversion process from various QT codecs to WMV for a client. The only problem I'm having with the actual transcoding is that the WMV comes out much brighter. This happens with not only Mac QT based apps but also Procoder on XP. I'm wondering if this is a gamma issue? I could set a filter to reduce the brightness before compression, but I don't think such a blanket 'fix' is the right way to go nor should it be necessary. Right now I'm tending towards using Procoder on a few P4s for the conversion, but am open to any other solutions to try. Ben already knows about this undertaking and suggested Procoder or the similar Carbon suite from Rhozet.
I just tried the PopWire WMV-9 export component for QT and it does not have the above problem. Using it does present a problem because current production boxes running Cleaner (!) would have to be used and also require lots of babysitting. Ugh.
You probably want to use Compression Master and some G5s then. As you noted in Popwire's WMV export plugin, the gamma issue isn't there, mainly because Popwire has the best filters and preprocessing on the market. Popwire's Compression Master 3 will allow you to do the batching you need to do that you could with Cleaner, only it would be more stable (Cleaner's fault, not the encoder's), and you would be able to do two-pass WMV encoding.
Actually, if you have that many files to encode, you probably should be looking at Popwire's more robust encoder called Compression Engine. It links with Compression Master and offers network rendering among other advanced encoding features. If time is of concern and these encodes have to meet a deadline, then I also suggest looking into a hardware WMV encoding solution, like that from Inlet Technologies and their Fathom board. Fathom can process two-pass SD to WMV encoding in or near real-time from disk-based files. For HD, two-pass is around 3 times real-time.