No, you cannot selectively unstack programs.
I was the same way, too, but I eventually got used to it. In the case of internet pop-ups, I let them accumulate for a short while, and then usually when there's about 5-6, I do a quick cleanup. If you want to keep your sanity in Windows 7, I recommend that you get out of the habit of using right-click menus to close windows. Closing via the context menu like that will make the stack preview pane go away, making you have to keep bringing it back up if you want to close more than one. Use the little X'es in the Window list, or better yet, just Middle-click on the ones you want to close.