I would suggest you to use one of the IAB standards : http://www.iab.net/guidelines/508676/508767/displayguidelines
In my case, i use 728x90 & 300x250. The most used banner size.
That right Alex. I suggest 728 X 90 . The most clicked size for my site.
Do you guys use an ad server (which one?) or your text boxes?
I use google adsense.
I use Google DFP http://www.google.com/dfp/info/sb/index.html