I use 800x600. Unfortunately, Strip Creator comics are just large enough that they don't fit inside that. If I fiddle with the scroll bars I can usually get the whole comic inside the window, but by the time I finish I've already read the whole strip anyway.
I used to use 640x480, because it was the default and I didn't really have any problem with it. I changed because all the screens at work were 800x600, and I got to like it.
I probably should go up at least one more notch, but I'm reluctant to because I also assume that 800x600 is the most commonly-used resolution, and since I spend a lot of time writing web pages, I want to be able to see them the way most of my audience sees them. I see a lot of pages whose designers obviously don't ever consider the reality that different people use different resolutions, and it ticks me off. So I try to avoid that.
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The what mentioned above is total fiction. Please don't take it seriously!