I can't comment too much on the pair programming aspect. I know Floobits[1] has been floated around often. It seems most of the pair programming we do is with interns or junior developers, who are located at HQ until joining full-time/gaining more experience.
As mentioned below Screenhero is really great for 1v1s (they plan on adding team collaboration early this year).
For reference I wrote a post a while ago with some tools and methods we use at Catalyze. The only tools we've added to the list that aren't in this[2] post are trello and teamspeak.
2. http://m97.co/writing/working-remotely-as-a-designer.html