I have been using Skype for a long time. What I like about it is that I can have it start up silently when I log on and quietly sit out of the way on my task bar until there is a request or a notice. The notices are little toast pop-ups and they are innocuous.
I have the same setup for Windows Live Messenger.
With the latest updates, Skype broke the rules. Now, whenever I log on, there is a Skype Home window and the basic Skype tool. I have to close them every time I sign on to my computer. There is no Tools | Option that gives me any control over this behavior.
Well, I have a behavior for that. It is called not starting Skype when I log onto my computer. There is an option for that.
Bye Bye …
Orcmid's Live HideOut 
Agreed. It’s been annoying the crap out of me. I get between two to three skype popups at random times throughout the day. Who does that as a company? Like is Word going to start randomly popping up? Is FireFox going to start opening itself?
What moron decided ‘Hey i know, lets constantly open skype on users systems so they can be reminded of…. how much they’ve recently started to hate skype? How is this good for marketing when people already have it installed? It probably just means skype is getting ready to blanket your system with advertisements. ‘This video chat is brought to you by Summers Eve’.
So now i just disable it altogether and only log in when I need to chat with somebody. Two-way video chat on cell phones/tablets will make skype outdated within the next two years anyway. Skype just seems anxious to get the ball rolling I guess.