There is no perfect ad placement solution suitable for every website. Nevertheless there are few guidelines to follow whilst working on a new page layout wondering where to put which ads.
I have been testing different layouts on 5 of my websites for the last 2 months. Back then in November the new ad size (300x600) appeared, and I was curious what to do with it.
Place a 300x600 advert in the sidebar above the fold, and your CTR will skyrocket. However as this is not a standard and widespread unit, we face more problems. Lots don't know about its existence, lots stay at the old solutions, and lots of designers are to be hired for this job, as a new ad has to be designed for the new dimensions. Therefore the competition is very low, which may be great for advertisers, but not for you as publisher. The CPC, the amount paid for a click is very low.
Placing a 300x600 under the main content is not okay, because most people scroll down and stop at the end of article / content. To see this huge ad, they would need to scroll another half screen. Why do they do this? They read the article and may take an action above the ad (press a button, signup for a newsletter, whatsoever), but they leave leaving this very large ad unseen.
Another reason to not use 300x600 text ads is that they contain 8 grey Adsense arrows, which is not so aesthetic to the eye.
Placing a 336x280 under the main content, however, seems to be very rewarding, as in most cases the whole ad can be seen. I wouldn't compare the color combinations for text ads, as on this spot, they seem to yield the same.
If the content container block is large enough, you can place two large rectangle (336x280) units following the article - for higher attention.
If the main content div is larger than 728px in width, you should use a 728x90 unit on the top of the article. Readers looking for the title will find it with their eyes and also being on the top it pays more.
Our aim is to place the better-paying ads to the top prioritising them. The one that is placed first in the source code, gets the highest CPC offers. Use a recommended ad size for this spot (728x90, 336x280, 250x250).
The problem with vertical units (120 and 160 x 600) is that people don't like to read any vertical stuff - I guess. If text ads appear on these spots, the prioritised ads will show up as text ads, and the less-paying ones will take up better units such as the leaderboard or large rectangle.
250x250 is great for sidebars.
468x60 banners are no longer as great for showing image ads as used to be. However, if you are in lack of space, use them to display single text ads, especially on the top, which is as good in CPC as 728x90. Since the ad headlines are small, use contrasted colours with blending solid background and no border.
Half banner ads (234x60) are good for smaller sidebars and should be placed to frequently used places such as next to a search box or login form. However, if these fields are likely to be misclicked, don't use them. Adsense requires every ad click to come by user interest. Half banner ads are often hard to spot, so I would avoid prioritising them.
The effectiveness of 125x125 / 200x200 text ads are gone since the grey arrow update.