That said, we're using HipChat now and love it. If you use Skype for group chat and don't use the phone a lot, I recommend the switch wholeheartedly.
I've logged in more than once to have a metric ton of IM's waiting for me.
If you use multiple computers it gets worse - if you send the message from your laptop it won't go through until the laptop and your friend are online again.
Its not a huge problem with a 1 on 1 chat, but with groups its frustrating.
We benefit greatly from having the chat room as sort of a canonical log of what's happening. Its nice to be able to leave a message for coworkers before you sign off for the night, and know that everyone will see it. With Skype we didn't have that guarantee.
It's kind of odd that they don't - messages are stored server side (have a bunch of conversations and then sign into an empty skype elsewhere - open chats are synched). You'd think this would be trivial to add.