I find that I get a lot better rendering times if I render to MPEG-2 in Sony Vegas when I'm applying effects than when I render directly to H.264 or WMV9. I could just re-import the MPEG-2 file back into Vegas and re-render as H.264, but I'd rather have something like Compressor (a batch transcoder) running in the background encoding the MPEG-2 file into H.264 while I get to work on the next scene in Vegas. Any recommendations?

You are throwing away OODLES of information going to MPEG-2. Why would you then go from this very lossy format, to mpeg4 which is lossy (though not as bad)?

You will get much higher quality going from your source file, straight to mpeg4.

Ervin Farkas did a bunch of tests and found that MPEG_streamclip gave the best conversion. I've been testing it on that basis and really like what I'm getting out

You misunderstand me.

I'm not looking for a particular codec to convert one file.

I'm looking for an application to convert multiple files in a batch.

As for why I'd render to MPEG-2 then H.264 - I probably wouldn't, now that I think about it.

There are loads of programs that can do that for you.
One product that comes to mind is Autodesk Cleaner. It has been used by many professionals for many years.

If you're looking for the fastest encode possible, check out Badaboom media converter. You'll need a Geforce 8 series or higher nvidia graphics card to use the program, but it will be the fastest encoder by a mile. I'm not sure if it does batch processing, and it's input and output file types are limited. However it will do h.264.

badaboomit.com

TMPGEnc Xpress, Sorenson Squeeze and Procoder will all batch process, and have H.264 support.