Pop-ups and new windows

Microsoft's 16 July 1998 SBN Wire (Site Builder Network) includes hints
on creating  confirmation boxes (ok/cancel pop-ups).

Do pop-up boxes create accessibility problems, and if so are there
recommended alternatives?

Along the same lines, what about the growing number of links that open a
new browser window when you click on them, or the ads that pop up in new
windows with no warning?

Many of the ads pop up at a specific size, and have all of the standard
browser navigation buttons hidden (in netscape at least). Does this
present any special accessibility problems? How important are the
browser's standard navigational controls to accessibility?

 -- Paul