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A couple of years ago, I did almost exactly what sjfan suggests, and it worked beautifully--but it took weeks, what with a few thousand mostly mystery and scifi books at that time. The main reason was I did not think it through first, as he suggests, so I had a lot of back and forth. I ended up with about 300 tags, which has not changed since. A lot of these are place names, so I can find mystery stories set in Italy, for example.
I tried the hierarchical route first, but that nearly drove me crazy. I find it best, for me, to have very simple tags, mostly one word, or two at most, so I have "Hard" as a tag rather than "Hard Science Fiction". The reason is, you can concatenate the simple tags with searches or virtual libraries in any arbitrary way, without having to set it up beforehand. You can find complex combinations you would never think of until you want them. Mystery stories that are also scifi, in the future, but not murder mysteries? No problem.
Another suggestion, install the Quality Check plug-in and when you're done, look for excessive tags. After renaming and some editing, I still found books with like 20 tags, many of then just plain wrong. Publishers will put any old tag on a book, I guess hoping to get a hit in someone's search no matter what. One I remember is one of Doc E.E. Smith's Lensman books as "Contemporary Romance"--Really?
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