heather,
I can tell you right now if anyone besides you has physical access to your computer you can throw any and all security out the window. Now, that doesn't mean that you should panic and run around like your skin is on fire or put on a tin foil hat. It is simply a reality, but at the same time the people in question would have to know what they were doing to accomplish such spying tasks.
I would first and foremost bring your concerns up with your roommate. I have had many roommates in the past and never will again in my entire life. I will live alone forever from now on, unless I get married, then I think i would have to move in with my wife....I am digressing though, so back on subject.
Talk with your roommate and be up front about it, otherwise it could blow up into a ridiculous situation. I mean if anyone could physically get on to your computer all they would need to do is look at your Internet history.
Some routers do keep logs and they can track what sites or IP addresses you are visiting. Most people don't know how to do this. Most people just plug the router in and if it works it works, and most people never even change the default password to their router.
If you suspect them of spying on you I would just talk about it. I once years ago lived in a 6 bed room 3 story home with all guys. It was a party house, and sometimes you had no privacy, so I know what you mean.