[gospastic]

You could always set up some kind of template guides layer which indicates to you the three common sizes, 800x 600 - 768 x 1024 and
1280 x 1024

(Actually, to avoid both vertical and horizontal scolling you might want to go for a lower stage/artboard eg: 740 x 450 instead of 800 x 600
and so on)

Checking your content with your template from time to time enables you to see which resolution is going to see what - and on the strength of that, place important items such as navigation in the 800 x 600 area, moving outwards. Does that make sense?

Another idea would be for your site to detect the screen resolution of your user, and display the content accordingly.