You can do all the things you are talking about with the AppleTV OS. You do have to enable afp and ssh, which requires removing the hard drive of the AppleTV. Then you can reinstall the AppleTV and login to the AppleTV using your computer. At this point you can install codecs to play other file types besides mp4. You can also install ATVFiles which would give you another menu on the AppleTV that would basically show you what files you have on your computer or an external hard drive. You could then play those with the AppleTV OS.
If you are not familiar with the terminal, I would suggest not even trying it. Honestly, I did all of that and ended up going back to a stock AppleTV. I did get a 500GB external drive that is connected to my Airport Extreme. I moved my iTunes library to the external drive and I can now play all my music and movies from the external drive without taking up all the room on my AppleTV. I have a ton of pictures that I have on the AppleTV and a crap load of Podcasts that I watch (DiggNation rocks) so I did upgrade to a 120GB AppleTV drive, but everything is streamed from an external drive in my office upstairs.
