So, I have a flash intro. It's the only thing on the page. It's designed to fit in a browser running in 800x600 resolution. Everything fits well, but in IE there's a blank scrollbar, in firefox, nothing. Now, when I remove the doc type the scrollbar in IE is fixed. So my question is, how do i keep the doctype and remove this nasty unnecessary right scrollbar?

Make sure your paddings and margins are set to 0 e.g.

body {
padding:0px;
margin:0px;
}

I take it that your flash intro is quite tightly designed for your browser size? Have you considdered what might happen if say for example, the user had an extra toolbar such as the google, yahoo! or MSN toolbars. Maybe, like me, they have all three? You should always design with a bit of slack just incase.