Unfortunately, if the existing window happens to be minimized, the user will not know that the anything has happened. One solution to this problem is to make sure that all your windows have different names. The trouble with this approach is that after a while, your user ends up with too many open windows. Another solution is to place a bit of javascript in the top of each page that you plan to open. If you are selecting a link for PopRocket, then you can use the file selector to pick a graphic file, a text file, or anything else that catches your fancy.
Graphics work really well.
Just size the pop-up to be the same size as the graphic itself. One trouble with selecting a file, though, is that you cannot use the onFocus trick described above. The file being put into the pop-up window is just a graphic and nothing more. There is no way to add javascript or any HTML to it. In that window, you can set size, handles, etc.