More formally known as the VideoLan Client, VLC is arguably the most format friendly media player you can download. The number of audio and video codecs it supports is phenomenal - both well known and obscure - and you can be sure that if other players shrug their shoulders at a difficult file, VLC will roll up its sleeves and get working. And it'll work with files created beyond the Mac: digital TV data pulled from your set-top box? No problem.
Squared 5 MPEG Streamclip
MPEG Streamclip does for media transcoding what VLC does for playback. It supports dozens of media container formats and codecs, and allows you to convert them from one to the other. And if there's a QuickTime plug-in for other formats, it'll work with them too - and with transcode accelerators like Elgato's Turbo.264 HD - reviewed here. All of which is just what you need to prepares video content for iPod, iPhone or Apple TV playback.
Free, open-source video transcoder. It just works and has some reasonable default template settings for the non-technically literate (like me).
I haven't had to bother with the Stuffit signup annoyances ever since I discovered "The Unarchiver", which handles at least as many formats (if not more) and is free and open source. The author seems readily available on his site to take bug reports and feature requests too, not that bugs seem too common.
Perian is a free, open source QuickTime component that adds native support for many popular video formats.