If you want something easy (but not free) you can use DivX Converter (excellent compression and easy pick of options). If you want something free and flexible (but more difficult) you can use Pazera. It uses ffmpeg as a back end. There are several versions of the software for various formats but I suspect that they differ in name only (I use flv to avi but it handles more than just flv).
The problem with ffmpeg is trying to figure out the command line switches and parameters. Pazera provides a GUI for all that and includes ffmpeg. You might want to look at VirtualDub which I also use. That does conversion as well as editing.
Since 2008, MediaCoder comes bundled with the OpenCandy software recommendation service which changes the classification of the app from freeware to nagware. During batch conversions once a certain number of conversions have been performed a window appears requiring human interaction (a simple CAPTCHA) to dismiss or pay a donation in order to remove the periodic nagging. ($15 minimum in 2011, $20 in 2012, $25 as of August 2013). You might want to check out XMedia Recode