Being able to have Skype on the iPhone run in the background is cool. However, as Stuart notes in his post Skype iPhone Multitasking Not Ready for Prime Time, there are problems in practice.
The biggest problem is your battery. Once you run Skype, it will keep running, and sucking up your battery. Instead of 5-6 hours of usage on my 3G S, with Skype in the background, I was getting more like 2-3 hours. As Stuart notes, the only way to stop it is manually from the iOS 4 multitasking (double-click) feature.
Skype should have a way to turn on/off multitasking from within the app itself. And as Stuart notes, when it is running in the background, you get barraged with notifications for everything and you have no controls over those notifications, short of quitting the Skype app from the multitasking bar.
The short of it is, if you start the Skype app, you probably want to double-click to kill it so it doesn’t kill your iPhone’s battery.