Subler is an Mac OS X app created to mux mp4 files. The main features are:

Creation of tx3g subtitles tracks, compatible with all Apple's devices (iPod, AppleTV, iPhone, QuickTime).
Mux video, audio, chapters, subtitles and closed captions tracks from mov, mp4 and mkv.
Raw formats: H.264 Elementary streams (.h264, .264), AAC (.aac), AC3 (.ac3), Scenarist (.scc)
iTunes metadata editing and TMDb and TVDB support.

@iconaholic You really should read this: Especially part 2, there's some sweet geek porn there.

Simple movie management for Mac

Sapphire Browser is a plug-in designed to take all the hassle out of managing media collections connected to your AppleTV. Sapphire has the ability to identify TV Shows and Movies simply by looking at the filename. Once identified, Sapphire will download show/movie information and cover art turning your stale file list into something worth looking at

Covers for Movies, Video, DVD and TV Shows

Covers for Movies, Video, DVD and TV Shows

MetaX is a meta-data tagger for MP4 files and their derivatives, as well as QuickTime movie files.