I use a couple of systems:
htmlrotate is available here: http://www.focalmedia.net/htmlrotate.html
its free and it does basic banner and link management

openX is the new version of phpadsnew, its available here: http://www.openx.org/
this one is much more complex and is the one that is used by a lot of people who sell ads as it does more than just banner/link management, it also does stats tracking too. This one is harder to learn and uses a lot more server resources to run.

Speaking of Blogs Organizer, those guys also have Links Organizer. I don't know if that one is good for multi-site banner management or not???? Also, I am sure there are other banner management programs available too.