I agree with Don that consistency is a good thing and we should do all one way or all the other.
However, I'll put my two cents in for the idea of having all the queries in the tcl scripts. I don't know if it could be reasonably accomplished, having given no thought to how it would be implemented, but strictly from a programming usability POV having the queries in seperate files drives me nuts. It's much harder to visualize what an unfamiliar piece of code does without being able to see all the code, no matter how well-named the query is.