I find the big square size ads usually get more clicks compared to the rectangle size when at the top of a post for my blog, but I think it can lead to a higher bounce rate since it is big, and can be annoying on lower resolution monitors like 800x600.
I also heard from people on forums, and blogs the 300x250 and square dimension ad units get more clicks since people are used to the large rectangular format.
But, the best way to get more clicks is to embed your ads very close to your content although it may annoy your visitors and they avoid your site.