The biggest difference is that HipChat is primarily about "rooms" and less about messaging individual people (although you can do that too). It makes for much better team workflow, because it enables a lot more passive information sharing. Most people in a room don't want to be actively involved in everything, but they would like to passively just see what's going on.

Secondly, it's centralized around a company, so you know that everyone has everyone else on HipChat, unlike Skype, where everyone needs to manage their contact list separately.

Finally, the notification features are really nice. I can just @mention someone's name, and it's like summoning them into the room to answer a question for me. It's way smoother than adding someone to a Skype conversation, since they'll be able to trace back the history of the conversation.