Is there a reference book that lists words by usage or theme?
Roget's Original Thesaurus was organized exactly that way. Its table of contents is organized by general theme; it is only once you traverse down to single words that he provides the set of synonyms.
I'm not sure if it's exactly what you have in mind, but you might try looking for a "thematic dictionary". One that I own is "The Longman Lexicon of Contemporary English". A search for "thematic dictionary" (including the double quotes) on Google yields lots of hits.