If you have that many books, hopefully a few of them are drm free?
So with DRM free books you can go to Calibre and try its 0.6 beta. Then tag your books with terms such as ScienceFiction (no spaces). There is an option in Calibre that adds tags to the book body. This option automatically appends the letters "ttt" to the back of the tag.
Now, you can search for funttt to find all of the books tagged fun.
The importance of the no spaces (ScienceFiction instead of Science Fiction) and adding ttt is so that you don't find hits on ordinary uses of the tag. For example, you don't want to find every book that has the word fun in it, just those that have the fun tag, thus funttt .
Thanks to Kovid for implementing this request of mine.
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