If you're getting FLV files from somewhere like Youtube and then converting them to MP4, then I use Miro (http://www.getmiro.com/) which cuts out the need to convert as it downloads files as MP4 files. When they're downloaded by Miro, they get put into their own Miro folder within your Movie's folder so you can nab them from there for sharing or putting on your iPod/iPhone.

For other video file converting I didn't find anything freeware or shareware I was truly happy with so I bit the bullet and upgraded to Quicktime Pro and that can do pretty much anything I need it to do with AVI/mp3/mp4/MOV files including converting and editing. For me, it was worth paying for