There are several things ...let's take a look.

Keep Your Banners Focused.
Don't use your home page for banners. Keep your banners focused on the page designed for that particular product. For example, a gardening site should display a fertilizer banner on the fertilizer page. Keep your banners, and text links for that matter, on relevant content pages.

Size of Banners.
Size does matter. Research has found that banners, normally those around 468 x 60 (pixels) are more catchy, gaining more clicks than the smaller pixel banners.

Banner Animation.
There have been studies that suggested animation can increase response rates by up to twenty five percent. It is important to note however, that flashing, obnoxious banners can have quite the opposite effect, especially if it remains in a position that is annoying to someone trying to read text.

Using animation banners would be better placed out of the range of text where a viewer can become distracted by it.

Banner Phrases and Wording.
A banner's choice of words is critical to its success. A good banner will demand a click by using attention grabbing words and phrases. Phrases such as 'Click here now', 'Buy Now', 'money back guarantee' all create a call to action . Words such as 'Last chance', 'only 24 hours left', or 'limited time offer' create a sense of urgency.

Asking questions that generate emotions such as 'Want to save money?', How would you like to be 10 pounds thinner?', 'Wouldn't you like to be debt free?' all are successful in promoting clicks. Be careful of using the word 'FREE'. While 'free' might generate a high C.T.R., the click to sales, however, is not as high.

Banners that ask questions instructing visitors to interact with the banner such as flashing an icon where the visitor can point and click has also shown to increase click through rates by as much as 18%.

Website Positioning of Banners.
Banners at the bottom of a page have almost three times the C.T.R. than at the top of the page. This is primarily because most viewers to a site are looking for information. Once they read the information they are more receptive to clicking on the banner after the information.

It's also been noted that banners placed on the lower right hand side next to the scroll bar had over a 200% increase in C.T.R.

Banner Loading Time.
Use fast loading banners. C.T.R. increases to nearly three percent when using banners that are about 3,000 bytes vs. banners over 10,000 bytes. You will miss out on clicks if it takes too long for a banner to load.

Refresh Your Banners.
Refresh your banners on a regular basis. I've learned that banners tend to lose their giddy-up after prolonged use. Even Yahoo! has mentioned that banners 'burn out' after about two weeks of use. Allow your site to change its look occasionally when promoting a particular product.

In conclusion, it's all about testing. No one can say for sure what works best. Tests are conducted all the time and theories are published, however only you can determine what really works best for you by testing it.