I have a single 1.6 TB partition to hold anime and another smaller partition to use for anime I'm currently downloading. As soon as its been downloaded I move it to the larger partition. This keeps the larger drive from becoming fragmented. It also reduces the amount of wear on the drive, thus reducing the chances of it failing (typically my archival drive is powered down).
Shows that I am currently fallowing (that have not been finished) are left in the archival partion inside its own folder. For those that have been finished I have a directory for
manga
anime that I have not finished, but have completely downloaded
anime that I have finished watching and have completely downloaded
"limbo" for anime that I don't want to delete, but don't feel like completing
a directory for OVAs and movies
a directory for trailers
and a directory for AMVs
Additionally, the directory for anime that has been finished and watched has the sub directories.
0-D
E-I
J-N
O-S
T-Z
Within each of those are directories for each series. For anime that have discrete seasons there is a sub directory S1, S2, ...
Limbo isn't well organized. Movies aren't given their own directory, but OVAs are. The trailer directory has no organization.
Thats pretty much it.
For for which episode I've watched, I just use my memory if it hasn't been too long. If its been a while I tend to watch a bit of the beginning of the show to see if I've seen it before. Searching takes a minute at most.