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You can also clean them up with the tag mapper. The main purpose is to create rules so that frequent offenders from metadata downloads are corrected and/or merged into another tag on download, but it also works on existing books.
You can make rules to remove extraneous tags, add tags to all books, or replace tags with another like
Replace the tag if it is one of: Dumb tag, Other dumb tag, Really dumb tag
With: Much better tag
You can find the tag mapper from the Download metadata dialog, or add it directly to a toolbar which works better on an existing library. When you press ok, it'll apply the current rules to all selected books, so once you're happy with your set of rules, just ctrl-a in the library and open tag mapper and press ok. And it'll apply the same rules to future metadata downloads, at least until you tell it not to.
I even use it as a cheap macro expander sometimes (you can load and save different rulesets on the fly). It's a vastly underused tool IMO. (But calibre is full of those).
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