I am currently in the process of creating Addin's and also converting our VBA projects to .NET addins. With the VBA applications, they would only work with specific MXD's. Is this possible to do with Addin's as well?
You can write your add-in to only respond to events when a specific document is open. CoCreate an MxDocument in ArcMap, cast to IMapDocument and check the DocumentFilename property to see if it's a map document you plan on supporting. It's extra code, but it works.
You can always implement an application extension and persist any data in the MXD, including some kind of flag which would signify that other parts of your addin should be available for that particular document.