Since we are very distributed company here at Automattic, we use lots of online collaboration tools including IRC, Skype, blogs, and wikis. The other big thing we’ve been using internally is a WordPress theme called Prologue that we developed last year.
Prologue is essentially a group twitter theme, and we’ve been hard at work updating it ( we are calling the new version P2 ) to include ajax updates, growl-like notifications, threaded comments, and a few other really clever features. It also looks great on the iPhone !
It’s available right now on WordPress.com, and will be available for self-hosted WordPress within a week or so. Definitely worth checking out.