I've wondered about this myself recently. And have resisted making some major changes due to potential organic rankings backlash. No one really knows. It's like the debate does having Adsense on your homepage potentially affect your rankings; I have never placed Adsense on the homepage for fear that it might be seen as a negative. Plus in this day and age the homepage is frequently under 20% of all entrance pages for a lot of sites. So I don't want to chance anything. Not to mention I think it makes most websites look less credible by having Adsense in a visible area on the homepage.
I am also resisting affiliate marketing as an alternative to Adsense due to the concern that it will harm organic rankings. Not that I have heard or seen actual proof.
OK, let's not get all paranoid about Google because as long as your site is designed properly and has SEO implemented correctly you should rank the same with or without ads, unless you do something stupid like plaster the site with ads, esp. at the top of the page pushing content below 'the fold' wherever the hell that is these days.
In other words, unless you've done something you would have a hard time explaining to Matt Cutts if he was reviewing your site, I wouldn't worry about it.
I you feel you might have to explain yourself, then worry ;)
Perhaps time that search and advertising should be separated
Unless Mr. Google has been grossly misleading us for a great many years [over a decade], that has ALWAYS been the case - at Google.
Wearing two hats. Google Search and Google AdSense - I've no personal experience, since ever Google arrived on the scene around June, 2000 [Yes that date] has Google ever been duplicitous in my personal experience.
Now if only I could reconfigure that bizarre Google Zoo. Panda, Penguin...