A user's request on the Adobe Forums prompted me to create this small utility that allows you to move all of the comment popups windows to the side of the page where they are located with a single click. This script can be used in both Acrobat and the free Reader.

The script can be downloaded (for FREE) from here.

Here's a page with a couple of comments that obscure the text. You can see the button the script added on the right, under the Extended panel:

And here's the same page after clicking that button. The popups have been moved out of the way, and then page is much less cluttered now:

As always, if you have any questions about this tool, or any other tool I've developed, you can contact me directly, and if you find this tool useful and would like to donate, it's always appreciated!