1) HipChat doesn't support audio only calls and conference calls. This was a dealbreaker for us.
2) Skype has a much larger user base overall and we can use it with other non-company members.
3) One of our developers wrote a plugin to inline images into Skype, which is a nice feature of HipChat.
4) Skype is free.
5) Skype's messaging is P2P and works in our office when our internet goes down. (Thanks Time Warner)