Video Converters

Handbrake is great. Change almost any file to MP4 or MKV file

http://handbrake.fr/

Check Format Factory too.

ffempeg

I was just about to recommend Super©, as I had good experiences with this tool in the past, but apparently they jumped as well on the bandwagon of shipping malware/crapware with their installers.

If it's mp4 + aac/ac3 (dolby) already, you can change the format w/o touching the audio/video. Use MKVExtractGUI-2 with MKVToolnix to extract video and audio file, then merge them to MP4 with a mp4 muxer. You can use YAMB, but I like My MP4Box GUI better.
If the video is not mp2/mp4/h.264 and audio is not aac/dolby ac3/mp3, mp4 won't accept the codec.

Virtual Dub

Freemake Video Converter is yet another option

XMedia Recode - It handles dozens of formats and has a bunch of profiles for different media players and phones, so you don't have to experiment what formats your device can handle.

Free Studio
It's very good, there is a all in one package with many other tools of them, too. All free, useful and easy to use.