You can use Avidemux to convert different formats together.Also you can have great editing features.
WinFF is another option only for video conversion.As the app site says:
WinFF is a GUI for the command line video converter, FFMPEG. It will convert most any video file that FFmpeg will convert. WinFF does multiple files in multiple formats at one time. You can for example convert mpeg's, flv's, and mov's, all into avi's all at once. WinFF is available for Windows 95, 98 , ME, NT, XP, VISTA, and Debian, Ubuntu, Redhat based GNU/Linux distributions.
ffmpeg is really powerful but it's a little geeky.WinFF is a GUI for it so it's easier to use.
Finally I found it.I couldn't remember the name.Mobile Media Converter is great to convert common video formats to mobile formats.
The Mobile Media Converter is a free video and audio converter for converting between popular desktop media formats like MP3, Windows Media Audio (wma), Ogg Vorbis Audio (ogg), Wave Audio (wav), MPEG video, AVI, Windows Media Video (wmv), Flash Video (flv), QuickTime Video (mov) and commonly used mobile devices/phones formats like AMR audio (amr) and 3GP video. iPod/iPhone and PSP compatible MP4 video are supported. Moreover, you can remove and add new formats or devices through the internet.
An integrated YoutTube downloader is available for direct downloading and converting to any of these formats. You can trim your clips for ringtone creation or any other purpose and crop your videos for removing up/down black bars or other unwanted parts of the image. Additionally, embedded subtitles can be encoded onto the video for watching movies or shows with subtitles on devices that does not supports them.
The program has a very easy-to-use and simple GUI (Graphical User Interface) that helps even the most amateur user. Most of the times, the only data that you must enter is the input file(s) or just drag 'n' drop the input file(s)! The 3GP and AMR formats are used by mobile phones for MMS, video and sound recordings, etc.