Realistically banners don't often convert very well in affiliate marketing, but they can be used in a variety of creative ways that could potentially earn you some hard earned affiliate commissions and also the placement of your banners could be a key factor of your banner campaigns.
I tend to look at banners as extensions of a product or service, a way to show that a business is serious an professional in it's approach with a quality graphic that displays the product brand, logo and motto. Banners can be used in a variety of creative ways in newsletters, email messages and mini websites to name a few, content relevancy comes into play here again as your banners must be totally relevant to your site as a whole and not steer away from your business brand.
In a blog for example, banners could be placed in the sidebar, although there is some debate as to the effectiveness of certain sizes of banner types, but the use of multiple banners that crowd and clutter your sidebar may not be worth it. Instead one skyscraper banner ad may prove better over three or four square banners that would have fit into the skyscraper banner.
If your blog is specifically for one affiliate program, then this could work better than anything else because your targeted content is written specifically for your single affiliate promotion and your skyscraper ad therefore would match more highly for relevancy.
On websites and other web pages, the wide format of banners could be used more in the form of a header graphic at the top of the page or as a footer to the page, these could prove quite effective, again if highly relevant so that your content leads into a banner to click, at the en of an article or content much like a text link, banners could help to visually split up the content and make it more scan-able.
Small micro banners are increasingly being used as powered by logo's which serve as banner logos to show what website, webhost or online publishing site you use for your affiliate website (Tip cheeky affiliate links work well here!)
What banner positions do you place your banners and why?