I think it's hard to replay without knowing your web site layout, too. But in my experience, Adsense Link Unit (5 or 4 links listed) under the menu has a good CTR, and often a good cpc.

336x280 text box, under the title of the content has a good ctr too.

Anyway it depends by many factors, your web site layout most of all.

From my experience one of the best AdSense formats is the leader board (728 x 90) placed immediately below the page header: this banner in this position has a good CTR

Give you an answer without knowing your web site is very difficult.

Here's some indication to run some tests changing the position of the your adsense units:

1. Insert the ads always at the top of the page, if possible, aligned to the left.
2. You can add one ads box immediately below the article text, this is good position.
3. The right column is where users click less
4. Draw the ads with the same colors and fonts used in your site
5. For the ads title using highly visible colors