Many of the sites I just visited say that the most controversial ad was the Focus on the Family done in 2010. The reason this ad is number one, is that Pam Tebow chose to have her baby against doctor's advice since she contracted amoebic dysentery while pregnant. The issue this raises is a woman choosing a pregnancy over the chance that carrying the child to term could kill her. This issue goes beyond the simple 'Pro Life' stance. http://www.oddee.com/item_97392.aspx

http://www.youtube.com/watch?v=xqReTDJSdhE

I have personally loved all of the Peta ads that usually end up getting banned.
Here is one from 2009.

http://www.youtube.com/watch?v=g0qawngQi6Q

Well it had to be the Focus on the Family pro-life Tim Tebow Ad. Oh, the horror of it all that pro choice folks might have to sit through an ad that celebrated a choice different from the one the champion. A courageous young woman choose to have her baby and that baby grew up to be a loving young man who is proud and thankful for what she did for him. How evil. Yet if you listened to the Pro choice (so long as you choose abortion) groups, you'd have thought the ad was promoting something truly wicked, like killing babies, maybe.

Planned Parenthood went so far as to run an opposing ad, which aired before the game, and the National Organization for Women (except pro life women) at least waited til after the ad aired, and finding nothing else to say, they attacked the ad as promoting violence, which is best responded to in one word: "silly". Tim Tebow fake tackled his mom, then gave her a hug and said thanks. It was silly, just like the doritos ad where a woman also got fake tackled but was never villified as promoting violence.

CBS was criticized by so-called pro choice (remember, Mrs; Tebow made a choice)groups and various other groups and individuals before the two ads had even been seen, and also after the airing, which is even more rediculous, since they were just about the most nothing piece of fluff imaginable.

The proof is in the pudding. I'll bet this answer gets the most argument (controversy) of any.

Oh, and the offending ad? Here it is folks, 30 seconds from Hell:
http://www.youtube.com/watch?v=xqReTDJSdhE

sources
http://collegefootballtalk.nbcsports.com/2010/01/16/tebow-and-controversy-super-bowl-style/
http://abcnews.go.com/Business/super-bowl-ads-tim-tebow-men-kissing-publicity-commercials-banned/story?id=9720930&page=3
http://knightnews.com/2010/02/sound-off-on-tim-tebow-superbowl-ad-controversy-abortion-planned-parenthood/