The bounty added (Oct. 2014) asks about a specific page, and ads like it:
Here is example page http://pjrvs.com/a/advice the add appears if you mouse past the top of the page, then sets a cookie to prevent reappearing
This is simply a DIV element hidden on the page that's revealed via JavaScript when the mouse moves out of the the browsing window.
Instead of worrying about disabling the JavaScript that reveals it, you just need to determine the element that will be revealed, and block it in your favorite ad-blocking program.
To figure it out for this example, I first looked at the cookie that prevents it showing again and saw it's key name was "viewedOuibounceModal".
So that tells me that it's probably a script referred to as "ouibounce", used for producing modal windows.
I then viewed the source for the page and located (near the bottom) the scripting that's controlling the modal popup. The script refers to "ouibonuce", "ouimodal", etc. quite a bit, so by what we learned from the cookie this is obviously it. :)
Just above the script, is a DIV element named "ouibounce-modal" with a class of "ouimodal". It contains other DIVS with the links and text seen in the modal popup.
I fired up AdBlock Plus, and added a custom element filter of "##DIV#ouibounce-modal" to block all DIVs named "ouibounce-modal".
Now the modal popup doesn't come back (whether I have the cookie or not).