The best way to prepare video for the Web is with dedicated (but relatively expensive) encoding software. Until recently, Discreet's Cleaner software had the market cornered in this area. But two new programs have emerged that are also worth considering: Canopus ProCoder and Sorenson Squeeze Compression Suite.
All three programs optimize the standard compressors for Web video and audio, and all of them do batch-processing to make it easier to save many video files at a time in one format or to create many format versions of one video file.