The biggest key, in my experience: find basic, reliable ways to communicate, standardize on them, and use them consistently. The biggest problems in remote work always seem to stem from people going invisible: no communication, no signs of work being done.

One tool that the OP doesn't mention, but should be a staple among companies of all sizes: Google Hangouts. You can make a permanent hangout using Google Calendar (search for this and you'll find how-tos). It's like a clubhouse, and it's really good for quick chats as well as full-on multi-person meetings.

For pairing, my team has been using a combination of Hangouts with tmux, which is an app similar to GNU Screen, but with next-generation features. (E.g.: when you split a window, or change to another one, everyone in the session sees it! Simpler configuration, too.)

We've found that this simple combination of live video chat with multi-user terminal access is actually better than working together in person. Both people can communicate easily, and no one has to move out of the way of the keyboard. :-)

edit: wording