This is (one of) the problems with prototyping outside the medium you are building in. Ideally, you'd be prototyping in the browser itself. That way you can easily and quickly account for browser variances.
Sans that, you really can only make a best guess based on the particular project you are working on.
For example, everyone in this thread is mentioning 960px. That's a fine assumption in a lot of cases, but a dangerous one in a lot of others.
Today, a good general size is 320px wide. In other words, mock up the mobile version of a responsive web site first. Then work your way out for larger views as needed.