I used to have everything together but long ago I started organizing stuff and now I'm much better for it.
For TV Series it's easy:
http://cl.ly/8IK0
All series follow the "Series Name/Series Name 1x/Series Name 1x01 Episode Title"
Where "1x" is the season, "1x01" is the season and episode and subtitles are stored with the same name and the language before the extension.
For Movies I've used several methods, but have settled on this:
http://cl.ly/8Idd
Since everyone at home goes to the movies server I have settled on greater genre classifications, with the movies inside. Three special folders are not by genre:
-TEMP: Recently downloaded movies.
-SUB: Movies with subtitles, but not organized into any genre.
-UNSUB: Sabe as above, without subs.
ES is for spanish movies (in spanish, too), "Animacion" are animated movies. Quick library for my daughter to reach into
, "Other" contains mostly DVD Documentaries or machinima. Nobody goes in there but me
The most important thing was to do a split at the top between movies and TV Series:
http://cl.ly/8JHP (the top two items)
I then created elsewhere several "OLDTV" folders, which contains canceled/ended series I will watch eventually (I'm currently making my way through Star Trek, for example). I don't keep them with the "normal" TV series because they're not watched as frequently and would only use up space in that server. They're not even shared through the network, but reside in my Time Machine disk.
All of this I access through SMBA in my DVR mediacenter, in the iPhone/iPad through Plex and on the mac with Plex.
I don't use any special tool for organizing. I just put things where they should be. Since I clean up all names (I *hate* having the original release names or RAR files, they're incredibly hostile to non-technical users like my mother, my wife or my daughter) it's not a big effort to put things in their places.
The only tool I do use, because I'm too lazy, is "TVRenamer", a Perl script that pulls info from epguides and renames the files. I helped with the modification to the program so it could rename subtitle files with language before the extension. I'm in the process of replacing this script with new functionality in SolEol.
http://www.robmeerman.co.uk/coding/file_renamer
Thanks to all this, Plex and XBMC-Based mediacenters are in paradise when cataloguing:
Movies:
http://cl.ly/8Im6
TV Series:
http://cl.ly/8JvQ
Old TV Series:
http://cl.ly/8IdG