On most of my hard drives (I have a lot of drives) I have an "Anime" folder. Completed series (as in "I have all the episodes") are placed in a subdirectory with the name of the series, while the files of theseries that are placed in the directory itself.
I Use FlexRAIDview to create a virtual drive that has the files of all of the other drives (if I have J:\Anime\x.avi and M:\Anime\y.avi then Y:\Anime will have both x.avi and y.avi).
When I accumulate 100-200GB of watched anime, preferably those series that will not have any more sequels or related series. I move them to a separate hard drive, change the subdirectory names to just the name of the anime (no more "[xyz]Anime_1"), organize the file names in each subdirectory, so if I sort them by name, the order of the files is the order of the episodes - nothing needs to be done if all files are from the same group, but if different groups did part of this, I move the group name after the episode number, so that this:
[abc] Anime 1 - 02.mkv
[xyz] Anime 1 - 01.mkv
(see, out of order)
becomes this:
Anime 1 - 01[xyz].mkv
Anime 1 - 02[abc].mkv.
I run the AniDB software to add the files to my anime list and verify checksums. If I find bad files, I try to fix/redownload them. If/when all files are OK I record that directory to LTO tape. LTO1 tape holds ~100GB and LTO2 holds ~200GB. I record whole tape at once and only of the anime that I already watched.
After that, I add the directory to my index (I use Advanced File Organizer) and delete it.
I can use AFO to find where any file is (on which HDD, tape, DVD).
I used to record DVDs, that they are less convenient (need to record lots of disks) and take up more physical space. A LTO tape in its box is only 11x11x2.7cm but holds 200GB ~45 DVDs. And I'd rather record, label and store a single tape than 45 DVDs. I recorded about 210 DVDs before switching to LTO1 and then LTO2. I am now slowly copying all DVDs to LTO2 tapes before the DVDs become unreadable.