I use On2's Flix - They have a version (Standard) for $39 that works well - The Pro version (about $199) is more functional with two pass encoding and such. It takes all sorts of video input (MPEG2, AVI, MOV, WMV, etc....) and outputs SWF and FLV.
I use the latest version of Camtasia - it encodes flash (conversion from .AVI files), even able to make 2-pass .flv files. It's become rather expensive unless you have an old version that you can upgrade, but it has it's own strengths for making videos of screen captures - I use it fairly frequently for making training videos on how to use software, or to capture camera moves in Google's Sketchup. All in all, quite a useful addition to my toolbox.
I write an avi from Vegas, then use the freeware Riva encoder to write the flv. It may not be the equal of expensive encoders, but it works just fine for my uses.