I've only put up the things that were already readily available as dotLRN applets, which means that a number of applications are still missing. There's a bit of work remaining in dotLRN'ifying all the other applications out there, which I haven't tackeled yet--but as soon as we get a client for this, we'd love to . That includes project management, hour logging, room reservations, form generator, company glossary, knowledge management, wiki, task list, workflow, etc.
Departments are groups, too, yes. The idea is that department groups are centered around departments, whereas the other groups will typically be centered around a project. I just figured that Departments were special yet common enough to warrant their own little special treatment.
If you built a collaborative to-do list and wrapped it to become a dotLRN applet, yet, it would show up in all the groups where you create an instance of it.
Regard dotLRN vs. OACS as the basis for an intranet, I think the dotLRN groups and portlets infrastructure is just subsites and OACS groupware functionality done right. If you want groupware functionality in your intranet, I don't see any downside to building on the dotLRN codebase.
I'll be on vacation for a week from now, but I'll be looking forward to your mock-ups.