Anti Virus scan - Reboot - exe file extensions...HELP!?

I had the Vista Internet Security Pop Ups, so I scanned my computer with AVG and SuperAntiSpyware and got rid of it. SuperAntiSpyware rebooted my laptop and everything seemed fine. Now that I go to open Skype, Yahoo! Messenger, Firefox or just even the Calculator it just recognize the file and asks me to choose what to open it with and non of the options work.
I then decided to do a system restore, but it does it with that aswell.
What am I supposed to do?? It only lets me open IE