Converting WMVs/RMs to Flash Video
 

This might be a groaner, so I appreciate any help I can get. My work has to convert several hundred videos for our new website. The problem is that for many of them, we only have WMV and RM versions and we need to convert them to a video format that can play on a flash video server (which means, I think, H264 or FLV).
Our criteria includes the obvious quality and cost, but because of the sheer number, we're also concerned about the ability to queue and the compression time for each video (currently 90 mins and around 30mb at 320 x 240). We tried Episode recently and had to return it because of consistent problems. What other solutions have people tried and what are we looking at in terms of the time per video?

Thanks.

encoding especially h.264 takes a long time. if you can split the encoding to multiple computer, for example 10 computers will do it 10x faster. or just farm out the job to someone who's setup to do it but i can't imagine it would be cheap.

Programs
 

We have a few computers we can farm them out to, but I'm specifically curious about what programs people recommend.