Pop Up Stopper from Panicware has a completely free version, which has a few less features than the non-free version but I've been using the free one for the best part of a year and its very handy. It kicks in automatically when you start IE/Netscape, then there is an icon in the bottom right corner (beside your clock) where you can turn it on or off as you need it.
I had Pop Up Stopper from Panicware installed before. The problem was that it prevented me from launching IE from the QuickLaunch bar.
If you're running an OS such as WinNT that has no QuickLaunch bar then I would certainly recommend Pop Up Stopper as a good solution.
Yeah I have that problem as well. well, it stops me from launching it from there if there is an IE window open already. Thats why I said you need to keep it handy and turn it on or off.
But as a "free" solution rather than a "free trial" I think its the best available
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You do NOT have to turn off Pop Up Stopper in order to lanuch a second IE window or to run IE from the QuickLaunch Bar . . just hold the 'Ctrl' key.