Dreamweaver will allow you to search the code of the entire site. If the site is setup properly including the RDS password and provide a data source it can tell you a lot of information. I've only set it up once so I can't remember exactly what information it gives you, I think maybe just the DB structure. Application window > databases. Even if it isn't set up properly just searching for "cfquery" will quickly find all your queries.
You could also write a CF script using CFDirectory/CFFile to loop the .cfm files and parse everything between cfquery and /cfquery tags.
CFBuilder may have some features like that but I'm not to familiar with it yet.
edit I've heard that CFBuilder can't natively find all your cfqueries that don't have cfqueryparam but you can use CF to extend CFB to do so. I imagine you could find/write something for CFB to help you with your problem.
another edit
I know it isn't indexing the contents of the query, but you can use regex to search using the editor as well. searching for <cfquery.+(select|insert|update|delete)
checking the regex box should find the queries that aren't using cfstoredProc (be sure to uncheck the match case option if there is one). I know Dreamweaver and Eclipse can both search for Regex.
HTH