Changing the color of the ads would be problematic, considering Google's stated intention of clearly differentiating between paid and "organic" content. That's why paid ads don't get mixed in with the organic listings on Google's results pages.

However, when it comes to AdSense (the ads that appear on content sites rather than search engine results), Google allows the site owner to make many changes to the look of the ads, and actually recommends using colors that make the ads blend in with the page's design. You're still required to keep the "Ads by Gooooooooogle" note visible, but they're clearly allowing site owners to blur the lines between content and advertising a bit.

Regarding branding, pay-per-click ads can serve that function whether they're clicked or not. That's why it's not uncommon to see a given site showing up in both the organic and paid sections of the same results page. The ad isn't there because the site owner failed to notice that they were ranking well for the keyword phrase; they're just getting their name onto the page as much as they can, with the understanding that most users are more likely to click the organic listing than the ad, so they're not likely to go broke on those ads.  

Thank you, Qwerty: very interesting to learn this viewpoint and to understand some of Google’s rationale behind the ads.