I'd go with 1024x768 considering as over the years, monitor resolutions have only grown bigger, and as 800x600 screens seem to be quite rarely used these days.
As well as many lower end PC monitors seem to still have at least a vertical of 768, as on my laptop.
Either one will work, although I doubt many people will have a 800x600 resolution monitor. For example, the monitor on an iMac G4, which is from 2002, comes with at least a 1024x768 resolution display. On the other hand an 800x600 base resolution could give a more retro look, if that's what you're going for.
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