EDIT. Putting this at the top for those, like myself, who look at new posts. Nothing to see here.
This post showed up while doing a google search 3 years later, so I'll just mention that the mention of ffmpeg vs ffmpeg1 is no longer applicable. The default version is ffmpeg in the 2's. This is a very old thread, and I'm only mentioning this because it came up for me while searching something ffmpeg/FreeBSD related on google.
I also edited out some now irrelevant comments that had to do with the manpages for the various programs.
The original, albeit edited post.
There's also ffmpeg. However, if you wind up choosing that, I'd recommend using ffmpeg1. The difference is that the original ffmpeg is an older version, 0.something and is much slower than the newer. I prefer it to mencoder, but do use both.
I think that
handbrake uses ffmpeg as a backend, but I could be wrong about that.
I have a page that some, though not all, have found useful, about working with multimedia files, at
https://srobb.net/dvds.html. (Most of the testing was done on Linux rather than FreeBSD, but most of it should be valid.) It links to, among others, a conversion matrix that might be useful, which is at
https://develop.participatoryculture.org/index.php/ConversionMatrix
