ImageJ normally only handles a single ROI (region-of-interest) at a time. This plugin extends the normal StackWindow class to handle an arbitrary number of different ROIs, each restricted to its individual frame in the stack. There is still just one current ROI, which has the normal yellow color and handles. All others are drawn in red. You can manipulate the current one as normal, but note that it doesn't vanish when you click outside of it. To delete it, you need to hit the 'Delete ROI' button on the panel that pops up when you run the plugin.
To switch ROIs, or just deselect the current one, right click on the image. If you right click in the outline of one of the red ROIs, it will switch that one to being current. If you right click outside of any ROI, then you end up with no ROI selected, whereupon you can draw new ones.
Note that you need to have the Java Topology Suite installed (you can just take jts.jar and jtsio.jar from the lib/ directory in their archive and put them in your JDK's ext/ directory).
To use it, just copy the contents of the plugins directory to your ImageJ plugins directory.