Worth the effort to get all your media nicely organised into folders with seasons and consistent names. Plex will then deal with it perfectly. I have about 2TBs of films and 1.5TB of TV shows on my ReadyNAS and can watch any of it from my iMac, MBA, aTV, iPhone or iPad from any Internet connection anywhere!
I am wrestling with this now as I transition my household from a PC to an all Apple environment. I have two ATV3s and I really like using them. I have alot of films and tv shows as well and would like to watch them in all the places you've named (except that I do not now what MBA stands for). To watch via ATV it has to be in iTunes so it takes Plex out of the mix. Is this correct? Is iTunes your primary or only serving application? This also means all films and tv shows would have to be reformatted to m4v or mp4, something I have been doing with Handbrake to date. I like what I see of Plex but just don't see how it would fit into my situation. It seems I would have to choose between Plex and my AppleTVs.
I would try iFlicks for converting all that video.
Just a bit of warning: as I've also pointed out in several posts here at MacRumors, iFlicks is considerably (about five times) slower than Subler and about three times slower than the latest beta of MP4tools. You might want to give a try to the latter two first.
About Subler. Is it normal that Mountain Lion wouldn't let me open it after unzipping? Something about untrusted software from sources other than the App Store etc. Handbrake had no such warning. Which I also didn't get off the App Store...
Here, the one at http://code.google.com/p/subler/downloads/detail?name=Subler-0.18.zip&can=2&q= could be opened and run just fine under ML.
That's where I got it from. So, your ML doesn't complain?
Nope - except for the usual "The app has been downloaded from the Internet" dialog, where you can just force running.
I haven't really hacked this ML except for disabling Quicklooksatellite (see http://cantuse.it/2008/11/disable-video-thumbnails-in-mac-os/ ) by "launchctl unload /System/Library/LaunchAgents/com.apple.quicklook.plist and deleting the four(!) plist files as is explained at https://discussions.apple.com/thread/2582860?start=0&tstart=0
Thanks for the reply. I think I found a set of options under Settings->Security. It says something about allowing Programs from different sources. I have it set to: App Store and verified Developers. I guess it's the "varified Delevopers" that restricts Subler from opening directly. Haven't tried it but I guess setting it to no restrictions would just warn about Subler being downloaded off the internet and then let it open just fine...
P.S. My OS is set to German language so I don't know the exact English words for the various settings and stuff.