I personally hate the Steam Chat messenger.
It's not as aesthetically pleasing (IMO) as Skype is.
I've had more glitches with it than Skype.
It never gives me the time at which a message was sent (bar the last message).
I can only chat to the one person at a time. (Requiring multiple steam windows in order to chat to two people at once, if we all want to chat together)
Everytime I leave a steam chat open and the person I was talking to signs in and out, in and out, I get loads of messages about them now being offline.
Perhaps I don't use Steam Chat enough and don't know about all the abilities it has, so if I'm wrong please forgive me, but it also doesn't record my previous chats.
If I've said something to someone and they've forgotten or what not, I can always go back to see what I said the other day or last week or month or what have you, so long as I am on Skype.
The only bonus for Steam Chat to me is the fact that I can use it while playing my Steam Games on fullscreen.
But if you're not likely to be playing your games while chatting to people, then I would go for Skype.
Skype seems cleaner and more managable.