It VisualStudio there is the Tool->ExternalTools command.
This gives an easy and limited way to add extra commands to the Tool menu.
VisualStudio also lets you do more extensive menu editing, but its a lot more complex.
SlickEdit, while it allows full menu editing, should provide a simpler way to add commands to the Tool menu, or perhaps a UserCommand menu.
Slick also provides Project->Tools: While useful, its very limited because it is specifically tied to a project, not a workspace or global.
I've only used Project->Tools to add custom commands a couple of times - mostly because it is so tightly scoped to a project.
I'd really like to see a more global equivalent.
The global commands should still have access to things like %r - it would just work with whatever happens to be the current project, workspace, file, etc.