I found a couple plugins that make the tag and category features function the way I’d like.

Simple TaggingThis plugin allows each post to have an associated set of tags. This enables a clean category system while still being able to show the subjects that each post talks about.
Simple Tagging Widget
This widget Enables a cloud [...]

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I’ve played around quite a bit with link structure for various sites I’ve programmed. I’ve found that Google will index your pages whether they have a parameterized URLs:
http://somesite.example?param1=this&param2=that
or parameterized Paths (Permalinks):
http://somesite.example/this/that
I think, however, that in general, search engines like the path portion of the URL better than they like than the query string for [...]

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