I know you said "free", but some programs I've come across are worth the price.
I love Wondershare Video Converter.
It'll convert almost every single video type to any other.
I've got to say, I'm really impressed with it.
You can even convert, say a music video, into just an mp3, so if you've found a song you like in a video and don't want the video on your iPhone (etc.) or the video on your computer period, but would like the mp3 of the song, it'll convert it (and quite quickly).
The only thing I wish they would change is offering a conversion of .SWF to other video formats. It's about the only format that it doesn't interact with.
Other than that, it's quite slick. You can put in hundreds of files, hit the Convert button and just let it go. Come back later and its done.
I'm really critical when it comes to software programs (and their inefficiencies or lack of functionality). Aside from the lack of .SWF support, I love this program.