To that end: when you link to a sponsored community, you'll see it listed with a green icon (that is, you'll see sponsored_comm instead of community). This icon will also be used in interest searches (more about those in a subsequent post) so you can scan through the list and immediately identify which communities are sponsored and which ones aren't.
More to come: separating them out on people's list of friends on the profile page (where there aren't icons next to the usernames).
More more to come: We'll be posting about other changes and answers to your questions -- stay tuned. And point your friends here, if they want details.