For music, iTunes. For movies, TV shows, music videos, etc., Plex, hands down. Plex can handle far more file types, automatically downloads artwork, metadata, subtitles, etc., can be controlled remotely with the Plex mobile app, easily plays content from any networked drive and deliver it to any computer, iOS device, etc. on the network. It can also play content across the internet.
This is my reasoning as well. I did try to use iTunes w/ ATV but found it clunky. Plex (on my NAS) w/ my Roku is fantastic. I only add movies to iTunes if I plan on syncing it on my iPad. Plex can also Airplay to the ATV. I just really like being able to play movies without having to use my Mac or have to carry an external drive. If I'm traveling, I can just stream it.