I don't have tools within the project. Tools are in a network share. Yes disk space is cheap these days but... come on :)
Also I have a database script folder below projectname (when it's a data driven app)
Of course it doesn't matter so much how you're set-up, but the fact that a logical organised standard is used to suit the project and adhered to with good discipline. This is useful whether you're solo or on a team.
