If you have Adobe Flash, you can use the Video Encoder that ships with it. If you're a Final Cut user, Quicktime Pro also has a setting to export to .flv
As far as free software, I know MPEG Streamclip (which you can get from http://www.squared5.com) has the ability to export as a .flv. The option isn't listed directly in the file menu. But under 'Export to other formats' it's a selectable option.