If your files are in one of formats supported by iTunes, then you could simply add these files to iTunes (without copying them and perhaps via read-only share/path) and then use Apple TV as usual.
If your files are in other formats, such as e.g. FLAC (lossless music) or MPEG2 (video, DVD) then you need to maintain a converted copy of your files in formats accessible by iTunes. This is what I plan to do, if I decide to use Front Row as my “Theatre View” in my living room, because most of my files are in FLAC, and will stay that way. A tool called dbPowerAmp Converter can convert FLAC (and other formats) into one of iTunes supported (and other) formats. This tool contains also a batch converter that can take care of entire directory tree. In my case, I would copy-convert to ALAC (Apple’s lossless) which is handled gracefully by dbPowerAmp, including embedded cover images.
People, including myself, have many times requested from Apple support for FLAC in iTunes. Knowing FLAC well, and a lot about iTunes, I would say that it would be a piece of cake for Apple to do. But they refuse; only God knows why. While things have improved a lot, apparently there are still some folks who don’t understand that openness gives you more than you loose by applying it.
It would be nice if the big (and small) vendors supported each others protocols and formats, or agreed upon one common. Unfortunately, this isn’t the case. Apple uses Rendezvous protocol, Microsoft uses UPnP, Apple uses iChat/AOL, Microsoft uses MSN etc, etc. Like small children in a sandbox – I don’t play with you because I don’t like you
