All of these suggestions (delete caches, restart, terminal commands, etc) do nothing to actually LOCATE the problem. They are just standard purging processes, and they have all failed to achieve resolution. And it is NOT Little Snitch either (tried turning that off and nothing changed). All these forums on this matter have been speculative and useless.
Ladies and Gents... I have found and isolated the ACTUAL PROBLEM. It is a Safari Extension that is doing it... specifically "VideoCatcher 5.3.8" which for me was installed with MovieSherlock. The extension adds the ability to download YouTube movies directly from Safari (by showing a small download button next to any embedded movie). When I remove that extension, all the annoying pop-ups go away.
MovieSherlock is not the only utility that does this however. There are several YouTube downloaders out there that ALL install an extension that detects YouTube videos on the page. I bet my hat that many (if not all) of you who are experiencing this pop-up issue... have installed one of those downloader utilities.
So, the solution is simple: disable that extension. If you need to download a YouTube video from a page, either temporarily enable that extension again as needed, or leave the Safari integration disabled and launch the actual utility itself and enter the URL into it for your download.
I would expect that MovieSherlock and the other YouTube downloading utilities will need to update their extensions (soon?) to deal with Yosemite's new browser script management.
PROBLEM SOLVED.