Not in my experience - I've been to several companies using Skype as the primary in-office communication tool and I find it really annoying. Skype is resource-heavy, poor on features and keeps breaking on Linux (management uses Windows, so it doesn't care, but I'm a dev...). I personally refused to use Skype this time (after it kept repeatedly failing on my Ubuntu machine) and made everyone send an e-mail or write me on Facebook if they need something. Works well (though I feel I'm missing on some amount of in-office chat).
I work in a relatively small company, everyone here has a private Facebook account, and I see no way in which Facebook chat is in any way worse than Skype. Both are closed-source, privately-owned, centralized servivces. But only one of them I tend to have opened anyway, as I use it to communicate with most of the people I know, and I can use it through Emacs when I find myself too distracted by the vanilla version.
Using FB at work is one thing, using FB to communicate with your coworkers another. FB is 'private' for me (as funny as that sounds - there's nothing really private on FB of course, but it's the social life outside of work that I refer to here). Not corporate.
