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Browser window size is the choice of the visitor, not the website. Making the website content flexible to fit no matter what the browser size is your best bet.
However I would recommend having an acceptably low view port resolution requirement for this. For example my site will work at 800x600 or greater. For example my site's minimally acceptable view port resolution is roughly 740x280. Mobile devices of course emulate resolutions and use other tricks to display pages better so it's important to keep mobile device support in mind.
Otherwise, don't do it. It is a nuisance as stated. I put it in the same category with untrusted sites and spammers. Not that you are doing anything bad, just the fact that it is annoying and I don't want to have to deal with it, as a viewer.
I'd assume you mean larger, probably for large photographs of something?
I like to leave a note that the site is best at 1280+ width if there are photos and such. You have no control. If you try to control it, remember iphones and cells, and such. You don't know who is trying to view, with what. If you try to fix a window size, other settings could override it anyway and just open full size in a new tab, depending.
Don't even mess with it. If you want 'picture-in-picture' stuff, or little panels or boxes, then I'd use those, not popup windows.
If their screen resolution is 1280x1024 though their viewing area is only 400x250 it would be acceptable ...
If I can't read it, I'll resize my browser myself.
There's a reason why I have my browser set to a certain size, and I like it that way.
[edited by: DrDoc at 5:51 am (utc) on Mar. 15, 2008]