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Here is my top tip.
Prior to adsense, Each of my article pages had an abundance of links. A huge sidebar full of links to each of the sections in my site, related and unrelated affiliate links, tools like recommend, print etc.
After adsense, I went after these links with a voracious appetite. I removed all but three links on each of the detailed story pages.
1. A "you are here" kind of navigation ( as seen in dmoz ) on the top.
2. An affiliate link at the bottom of the usually full page review.
3. Adsense ads on the right.
Thats it. Nothing more than three choices given to the user.
By reducing the number of options given to the user, I doubled my amazon commission as well am maintaining a great CTR with adsense.
My only cause of worry was the number of page views per user on my site, which incidentally went up :-)
And the clean design greatly improved the look and feel of my site according to my users.
Simply put, Reduced options ( links ) : More clicks and better usability.
So what is your tip?
Whitespace, cleanliness, clarity. Remember people can usually only take in one message at a time, so make sure you dont give them more than one on one page.
mallu i think you have summed up the best tip of all for getting good CTR. The only others i would metion secondarily are putting the code "above the fold" but still viewable with other content next to it (this is why we always use skyscrapers), and giving the ads some impact (make them look "important") by positioning and color scheme.
Of course the other thing is making sure you have tightly focused pages so the adsense robot can serve up relevant ads.