When you click on an Adium Growl announcement, the focus flips to an IM window with that user, so I can type at them immediately. But when you click on a Skype Growl annoucement, it just flips over to Skype, and the focus is on whoever I Skype chatted with most recently, not the person announced by the Growl bubble.
This is very confusing.
The most common oops case is when I see my MySQL PS scheduler come online when I have a message for her. A couple of times, I've seen the Growl bubble, and just instantly clicked it, typed my message, and hit return, and sent a confusing message to someone else. Fortunately, there have been no major mavs or client NDA breaches. But I do wish that Skype would fix that.
I also wish that both Adium and Skype would let me selectively enable Growl notifications on a group or individual basis. I like the Growl updates, but I don't need them for everyone on my contact list.