1script - 5:30 am on Apr 24, 2012 (gmt 0)
In hopes to cheer up a fellow webmaster, here's my (limited as it is) experience in messing with ads:
Site got banned (completely de-indexed, zero G traffic).
Site had two super-prominent 300x250 ad blocks ATF. Not saying it was the reason for the ban!
Replaced the two 300x250 blocks with one 728x90 ATF and one 300x250 in-content. CPM dropped about 20% - painful but bearable.
Done one or two cosmetic changes (font size and background colors, mostly stuff like this in an external CSS file). No content change whatsoever.
Submitted re-inclusion request.
Three weeks later received a Gmail (not a WMT message) response saying, in essence, "we see improvements but one or more pages of your site still violate ..." (emphasis mine)
One month after that (no changes in the interim and no communique with G) side got un-banned. Mind you, G traffic is still laughable (almost nil). But WMT for this site works, Gbot crawls and everything looks peachy except, of course, the site is still heavily penalized.
The takeaway, I think, should be this: the ads do matter. Mostly, from what I can tell, to the human reviewers (or members of the search quality team, whatever). I don't believe Panda or any algo change has anything to do with it. A person with the power to ban or penalize you lands on [one page of] your site, after 0.2 sec still hates it - you're toast.
So, if you're planning to submit a re-inclusion request, and we all hope that this generates at least one human visit from Google, you do want to tone the ads down if they are absolutely glaring. If you think that you're not dealing with any manual action against your site, messing with ads is not going to help, might as well leave them alone. Or tone them down for the benefit of your users if it makes sense to you.