For what it's worth, as an average developer, I'm am often frustrated by the necessity of opening so many files to find out how things are working.
I like Don's suggestion of putting all queries back into the .tcl file, with switches for the sql for different databases. It would make code more readable for me, since the sql is situated in the context of the file where it's used. Also, it would be much simpler to port one-database files to multiple, since everything is right there in one file instead of spanning up to 3.
When I develop for my own local sites, I almost always put queries in the .tcl file. Going through the hassle of separating that out doesn't give me any benefits. If, as has happened with others, such local code is deemed applicable to the larger toolkit, that sql must first be pulled out of those .tcl files into the appropriate .xql. I think flags for the db_* query handlers would greatly ease the road for code contribution by eliminating the need for this step.