Open Atrium 2 is good, despite also being complicated. I recently launched an intranet with it and I'd say the baked-in features make it worth the effort.
Spaces operate as your 'subsites' would, with their own members, content, permissions, etc. Have a look here for some basic info.
You can also set up an Open Atrium 2 instance with Pantheon in about 10 minutes, so it's easy to try out!