There seems to be a widely popular blog post (here) about creating these. It's tailored to SharePoint 2007, but I've read through the entire article, and it makes sense. I've followed the directions, but the emails that come through don't contain any of my changes.
I've also followed directions and code to change the alert template for a specific list (done through the object model). And after I make the changes, I can get to the list through the object model and verify that my changes are saved in the AlertTemplate property for the list - but the changes don't actually come through in the alert emails.
And finally, I've tried adding a new NotificationHandlerAssembly to send out a completely custom email, but the custom code in my assembly doesn't get called and my email doesn't go out - with no errors present in the Logs.