A "bad" program on the HD that is just in a random folder shouldn't effect it at all. The only programs that get loaded at startup are the OS files and whatever Extensions and Control Panels that you have added to the System Folder. Uninstalling Extensions and Control Panels is as simple as dragging them from the System Folder and placing them in another folder or the Desktop. This allows you to pick and choose what loads at startup.
I'm getting ready to motivate myself to do some testing in the basement. Probably, go sit down in my museum, watch the Wings game, and set my Plus up.