I do a fair bit of video editing and I have 3 recommendations for you.

OSS VIDEO CONVERTER http://www.onestopsoft.com/video-converter.html

this program does excellent batch files and can convert from avi/mpeg to wmv, rm and mov quite well. I prefer the wmv becuase of the streaming properties on a windows media server box. It can do any web compression from 56K to 1MB and can do it quite easily and fast. It is shareware for a trial but purchase price is really reasonable.

DISCREET MEDIA CLEANER XL http://www4.discreet.com/cleanerxl/

This ia a bigtime program with more bells and whistles than some NASA programs. it will likely be too much for you but you can find some fairly inexpensive versions of it online. It does everything from watermarking, audio and video normalization, compression, conversion, cropping video, batch conversion, multiple jobs to different types of video conversion etc.

AVID VIDEO http://www.avid.com/products/video/

This is a mega expensive program but a standard in the video editing industry. go to their website for the full details as books are written on this software, I cant fill you in on it here.

I hope this help you.