I'm totally OK with that actually. Organic sponsorships have the very important quality of being vetted by the site in question, which greatly lowers the risk of malware being delivered in a way that the site owner can't claim responsibility over. I think tracking of these types of sponsorships would also be fairly trivial (server-side code to report back pageloads or even access to youtube's analytics for sponsored videos) and shouldn't need to involve third-party software running in the user's browser.

It's third-party javascript (and flash) that I mostly object to. If the site owners have to serve the script in question, they can inspect it for shady behavior, and make informed decisions. I believe the practice of tossing a third-party iframe in your template/css and calling it a day is the most dangerous trend on the web right now.