The sites that I run suffer from ad-blind visitors. I find that occasionally repositioning ads will heighten visitor awareness and bring about a short term increase in clicks. As my sites are fairly low in traffic I don't have a big enough sample to be sure about the best long term position.

Can anyone give me some sort of indication as to what I can expect in terms of CTR?

Want to flip a coin? Consult the Taro Cards? Study your navel?

All are equally as good as to any opinion we can venture.

what I can expect in terms of CTR

Nope but I can nearly guarantee you will see a big increase if my metrics are anything to go by.

All you can do is test. Unlike HuskyPup, I've never gotten the 728x90 to perform well on any of my sites (even the 728x15 link units outperform it for me)

A leaderboard definitely worked better for me. When I switched to a wide skyscraper on the right side--and later to a medium rectangle on the right side--CTR dropped noticeably.

I love the look of the 728x90, however no one ever clicked on it, no matter what my site looked like otherwise or whatever the niche was about.

I stick with 336x280 on most all sites as that does best for me!

I love the look of the 728x90, however no one ever clicked on it, no matter what my site looked like otherwise or whatever the niche was about.

And I had the opposite experience, which just goes to show that testing is the only way to know what will work for a given site. Fortunately, it's easy to test ad sizes with AdSense, assuming that your ads aren't hardcoded into individual pages.