I once had to do something vaguely similar. I needed to open a GWT app
in a window from a non-GWT app. I called var win =
window.open("GwtHtmlPage.html") and then set the data the GWT app
needed with win.blah = 3 or whatever. Then my GWT app used some JSNI
to fetch that value.
The problem as Robert metioned is that GWT doesn't really want you
doing inter-window communication. So you have to sling your own JSNI.
Derek