I was first recommended FormatFactory by somebody who reviews a lot of software (writes articles), It"s actually quite good, and Free. The UI is a bit confusing though. But i"ve used it many times.
Except that, like almost all such "freeware" programs, it is in violation of the licenses of its component parts (libavcodec, ffmpeg, mplayer etc.). They"re shipping binary executables (possibly modified) and profiting from them without providing sources or proper credit / copyright notification as required. I"ve no idea why C|Net and the like accept to host these files. It"s blatant copyright infringement. We should demand that C|Net be shut down permanently a la MegaUpload for directly supporting commercial copyright infringement…
When something as great as Handbrake exists that actually honours the licenses, and is itself open source, I see no reason to use a solution that"s ripping off the decades of hard work by the open source community.
tl;dr +1 Handbrake
Now, Now, let's not get all SOPA. xP Kidding. Though, I never noticed this before. Interesting. Also should look at handbrake. xD