OS X :: Unable To Launch Applications On Mac 10.4

Background: A day or two after plugging a USB that had been plugged into a virus ridden PC into my Mac, the internet went berserk. My father told me that he thought it was the USB that had messed the internet up. A few days later, he said that the USB was fine, it was just that Apple came out with a Security Update that changed our router access password (we cannot access our own internet because our password was being changed by a "Security Update"). So, in a kind effort to provide internet for me, he went into my Account Settings and changed my permissions so I was able to access the Application "Internet Connect". Well, I was able to run the application and connect to our internet, but I couldn't launch any applications that didn't either: a.)Come with the machine or b.)Need the administrator password to install.

The Problem: I cannot launch any applications that didn't need the administrator password or come with the system. I AM able to run Apps such as iChat, iTunes, Ventrilo(required administrator password) and Quicktime. I AM NOT able to run any of the games that I have downloaded, teamspeak, transmission, teamviewer, or any .dmg file. After two weeks of looking for possible causes and trying everything in our power, my dad and I can't find the cause of this. He has taken off all parental control and given me control of everything on my account, but still I can't launch anything.