One thing that still annoys me on occasion is when websites throw up popups, especially those that come up behind the main browser window. In particular, on OSX you have to either Command-tilde, Command-W to get to the window to close it, or pop up Expose/Mission Control or right click the Dock icon to hunt down the window. (Window 7's taskbar peek feature is actually pretty useful in this instance without forcing you to switch contexts.)

Since my browser window is not usually full screen, a much more simple solution for me would be for Chrome to line them up in a way that you can close them quickly if they are likely to be unwanted (as most background popups are).

Here is a quick animation to help visualize the problem. When you click on the window on the left, you see that popups are often occluded, where as in the other case, you can just close the windows one at a time without having to change context as much.



Of course, the ideal solution would be to prevent unwanted popups from showing at all. :)
In other news, welcome to the new Labs-in-posts!

Edit: On second thought, an even simpler interim solution might even be to add a context menu item on the tab such that when you right click, you can "Close all spawned windows" from the current page. This would solve the issue for full screen windows and is less intrusive and more context specific than the possibilities using the generic system window manager.