The portal connection is pretty useful, say you have a web application for team sites and have self service site creation turned on you would probably like the portal connection to be set to your portal homepage. Just as a refresher the portal connection is the link at the top of your site:
I've put together a tool that will give you the ability to set the portal connection for new sites and also for newly created sites. Once the solution has been deployed and the features activated, from central admin you will see a new link:
Following this link you will be presented with the following page:
From here you can select the web application to work with and you can set the portal name and URL. By selecting the 'Apply To Existing Sites' checkbox, you will set portal connections to all the sites on that web application.
The SharePoint solution can be downloaded here, I'll be releasing the code soon, I want to release it to Codeplex, I just need to set it up first.
Here is a small screencast showing the tool in use
Edit: I've now setup the Codeplex project: http://codeplex.com/SPPortalConnection