Multi Domain Links Organiser is undoubtfully the best you'll find around. Yes I use it, the majority of webmasters does. And I think we all pretty much agree that it is the best linking script to date, also because it got a setup for auto interlinking, a-b-c-d linking etc. And ofcourse, it's multi domain. Only 1 install needed and you can use it on any of your websites, without installing it on every server.
It will generate includes for every website you set up. SI or php include the files and you're done.