Fair Use Wizard, Gordian Knott, and Auto Gordian Knott (xvid and h.264) - Free. Prmarily intended for conversion of DVD files to xvid/h.264.
Windows Media Encoder (WMV9) - Free. If you can play the file in Windows Media Player, this utility will encode it to WMV9. Pretty flexible program, if not a little buggy on large files. Very easy to use wizard for novices.
SUPER GUI + ffmpeg + mencoder + x264 (h.264) - Free. Very flexible system. Will convert just about any video file to h.264. May be a bit confusing for someone who doesnt understand all the settings and terminology.
Nero Recode (h.264) - Not free, but if you already have the newest Nero software bundle, then you already have this.
Quicktime Pro (h.264) - Not free, and very slow.