Yup, Growstuff uses Skype + Teamviewer (or possibly tmux if both people are working on the same linux box). There's more detail about how we do it at http://wiki.growstuff.org/index.php/Pairing

The app we're building, Pear, is basically a matchmaking service for people who would like to pair program together, because we found it hard to keep track of who was interested and what timezones they're in. You can find out more about it at http://wiki.growstuff.org/index.php/Pear or see it in (fairly low-key) action at http://pear.growstuff.org/