This is something I used to run into with my college roommates. It's all too easy to go from "Is this your bowl in the sink?" to "Yea, but you leave your clothes in the washer for days, so who cares?" to a downward spiral with no end.
In my years living with messy people, my chief advice here would be to ask yourself:
What's your actual goal here?
Certainly it's not just to accuse your coworker of using your computer and then be upset with them. More likely, you're probably asking so that you can lay down a boundary and let them know that you don't want them doing something like that in the future.
So instead of trying to figure out whether or not they're in the wrong (which will sound accusing no matter how you do it--you're trying to accuse them after all!), approach this by trying to solve the deeper issue. Regardless of whether or not they used your computer, that's a boundary that you want to exert.
I may say something like:
Hey Fred! I know different people have different feelings about their computers and that I often leave mine lying around. I just wanted to let you know though that it makes me uncomfortable when other people use it without asking me. If you see anyone using my computer when I'm not around, could you let them know? Thanks!
This does a couple things--it let's them know how you feel about your computer and what your boundary is. And it also avoids accusing them by recruiting them to help enforce it. In fact, you're even putting them in a position of trust here--quite the opposite of an accusation!