Well, Brianna it might indeed look like a can of worms but it is a useful vehicle for a dialogue which might help many users.
Michael's analogy is excellent.
Skype uses a relatively sophisticated method to maintain state or semi-state and p2p protocol (used in KaZaA) successfully enables operation even where both users (to the call) are behind NATs. It does this by hole-punching or reverse connectivity by initiating direct contact with a supernode at startup and later opening multiple TCP/UDP connections. This serves as a routable address. After all, that's how you know when another Skype user is trying to contact you without you initiating the call! Magically, the computer 'rings' to signify an incoming call without you making one! To do that and to increase call quality it prefers to use a NAT/ router which is 'p2p friendly'. Reportedly, over 75% of routers are 'p2p friendly' and permit this traversal. My own investigations last year revealed that most 'home' routers are 'p2p friendly' by default.
Further, Skype is also very helpful by opening all these capabilities for you and updating its own software without intervention by you. As such it is a security risk to some and not to others. I can only speak for myself and say that I could never allow it to exist on any of my systems even though I accept that it is popular. I tested it (in the UK not here in the USA) and quickly became a supernode.
Most system degradation for home users appears to be caused by a flood of connection requests causing delays in your own work. These can be reduced if you shut down your computer periodically, or only start the Skype application when needed...then shutting it down completely when the call is terminated. Certainly, avoid having it start when the computer is switched on as it will run in the background.
The fact remains that Skype continues to be highly popular. Indeed, a few of my colleagues still use it. I see nothing wrong in that because they are only online for a few minutes at a time before closing.
For general use I highly recommend Yahoo Messenger as it also incorprates elementary one-to-one video connectivity. For full, no-cost video-conferencing, use EVO/VRVS. For all other VoIP, I continue to recommend SIP. Cranky old-timers like me prefer two tin-cans and a piece of string...but only when we know we can cut the string after the call! Have fun! Stay aware!
http://www.us-cert.gov/