I've been using Skype for quite a while now as a way to communicate in an agile environment. It's pretty good for communicating but I've also found that Skype tends to limit face to face communication. Many times I've Skyped the person right next to me or at the next table just because I'm too lazy to get up and talk or I didn't want to disturb the person when they're listening to music.
I've also found that twitter may be a way to say what you're working on but again, it can limit true collaboration. People tend to rely on the technology. It's a psychology thing - developers tend to be introverted and comfortable with technology (a generalization).
So what do we do? Hold meetings (no)? Get rid of Skype (no)? I'd suggest that we slay the dragon by specifically pointing out that the tool can be a problem for face to face collaboration. Being explicit about the problem can keep people on the striaght and narrow. Face to face collaboration is certainly the highest bandwidth for communication. When you find yourself using Skype too much - pinch yourself and vow not to do that again.