I use these for my "non QuickTime / iTunes" media files:
Plex
MPlayerX
VLC
Plex
Best HTPC solution. Supports all formats I throw at it, regarding HD Movies, TV shows, etc. (MKV, TS, AVI, WMV, and AC3, DTS 5.1 audio, etc.). Needs a Plex Server (Mac mini in my case) and Plex Home Theater.app (on another Mac mini with HDMI in my case) connected to TV / Home theater system.
MPlayerX
The easiest to use single app to watch movies, and also supports most (all?) movie-formats I throw at it. Also the fact that you download it for free in the MAS makes me like this app.
However, High-quality audio tracks (24 bits, 96Khz and higher) seem to have issues.
VLC
I use this app for the High-quality audio tracks (24 bits, 96Khz and higher) which other apps cannot play (well).
In short, I use all three.