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The first approach is the obvious one of using one of the Access databases made to keep track of "comic books".
A 2nd approach is to use one of the user-made comic book programs. Some are "pay for" but there is a donation-ware one that has jumped to the forefront. It is usable for doujins even though doujins need more datafields than USA type comicbooks do. It supports user-made scripts and you can download those via their forums. If you tweak a script and make it better for doujins, please do upload it so that the tools can evolve as different people try improving them.
You should standardize the format of your filenames before you click-to-enter them into the database. So try:
hxxp://doujinrenamer(D0T)wordpress(D0T)com
..and please leave comments to encourage the author to keep working on it. The tool also checks and uses the mugimugi doujinshi database for names.
Standardized names let you use search templates to scan thru your database (such as hxxp://comicrack(D0T)cyolito(D0T)com) instead of just returning hits for the same keyword regardless of author, circle, title. I tend to use the format [circle (author)] doujin_title (source_or parodytitle)(C79){color}{decen ghost}{LQ HQ SHQ UHQ}[scanlator_group1,scanlator_group2 person person perso].rar
[Aoi Hitori] Horoyoi - A Bit Drunk [Steve+4chan]rar
[Distance] HHH Triple H {Decen H9Eleven}[Sling,Strange Grey Cat,Yoroshii].rar