We're still using Skype and starting to introduce irc.
One main advantage that Skype had going for it was a little known feature on the Mac Skype 5 and 6 clients: ChatStyles [1]
The Mac Skype client used a copy of webkit to render the conversations and at one point provided instructions to let you hook into that and style the conversations the way you like with HTML templates, css and javascript.
We took advantage of this feature it to add communication short cuts, the main example being that if someone typed #1234 in a chat and the person receiving the message was using our ChatStyle #1234 would become a clickable link to the appropriate bug in our issue tracking system.
Skype silently killed this feature in an update a few weeks ago, so our thought is to go with IRC and and use an IRC bot that can provide these kinds of shortcuts.
If there is another chat system that allows you to customize these kinds of things, I'd love to hear
about it.
[1] http://joemiller.me/2011/05/24/alternative-skins-for-skype-5...
