For encoding from whatever your source format is into files for web use, I recommend Sorenson Squeeze. It does batch conversion into most commonly used formats, including Real Media, Windows Media, Flash, Quicktime, and a number of others.

You can set all of the conversion specifications for each file type, set up multiple conversions (such as WMF low bandwidth, WMF high bandwidth, Quicktime low, Flash) in a batch file, and then set Squeeze to look at a particular directory and start converting whenever it finds files there.

It also seems to be much faster than the encoders in Premiere (which we use).