On the right there is "issues" and "custom queries". The custom queries only show up on the projects they apply to.
I extensively use custom queries. Since there seems to be plenty of real estate on the right, it would be helpful to me anyways if there was another group for "links" (or named whatever). If there were a way to add my queries tied to a project over there (perhaps in settings) so I could quickly switch between projects with custom queries, that would be great.