In content links usually work best. Some of my banners do get a 10% to 25% CTR. I don’t clutter the site with a ton of banners. Just a few in rotation. I get better CTRs this way because it gives users less choice on where to go.
To track click through rates on banners, I use http://openads.org Throw a bunch of banners into rotation then after every couple hundred visitors, check the click through rates and drop the ones that are the lowest. Add more for testing and try out different locations.