I have an excel spreadsheet set up so I can sort the list in multiple ways. Generally the list is sorted by name (some are in Japanese, some in English). I track:
- if the series is complete
- the author/artist name(s),
- the file folder it's stored in
- the scanlator group name(s)
- the genre
- .
No, I'm not wrapped too tight!

Mine is a hot mess. I have most of it shoved in a folder, and the newer stuff goes into my documents folder so that I can keep my desktop clean and find the stuff that I'm currently reading. I have WAY too much. I actually lost most of my mangas when I switched computers. I put them all on CD (it took 20! 20 CDs!), but they got damaged during my super long drive from California to Texas. Apparently, the daily 100 degree temperatures in Arizona are not good for them. (>.<)

I'm thinking of getting a zip drive and putting all of my completed mangas on it so that they're safe. It'll be about $100, but it's totally worth it compared to all the precious mangas and anime that I'll lose if something (else) goes wrong with my PC. I bet there are much cheaper drives out there, even.

I think I will organize them under the mangaka's name (like you do) when I get around to it. Right now, I just do a search for stuff that people have asked for, and grab it from where ever I find it on my box. It's a sad state of affairs, I know.

First in my documents it's in 'Manga'
It is then separated into categories by genre like 'Yaoi' 'Artbooks' etc...
Then it's a mess in there organizing it from the time it was modified so newest at the bottom.
I'm trying to start organizing it by author...that is if I have two or more from an author.

My doujinshi folder is simply organized by what manga or anime it's from and in alphabetical order.

Oh, gosh... Wonderful question! BTW, I have about 100 GB yaoi already. I have folders Scanlations, Animes, Novels, OST, Games and CD Dramas. I sort the mangas by scanlating teams. That is the only way to have any organizing. This way I just add the next release of the particular sc team. I also have subfolder LJ where I dll from LJ users. In this subfolder I have other subfolders with the users's names. I have few subfolders named by search engines like 4shared, mediafire ect. and in them I also separate the mangas by the name of the uploader.

organized them in specific authors folders (i'm author oriented), and i burn the ones that i have read more than 10 times on DVDs

I used to be better. Had a folder and then listed it by author. Then I had a spread sheet that said the story, author, what group scanned it. I ketp them all on an external drive.

I haven't updated my list in probably a year. Now I got a bigger external drive that I want to move them all to. So maybe As I am moving them I will update my list again.