I recently put together a bunch of guidance topics for Microsoft Patterns and Practices for doing ClickOnce deployments of CAB-based applications. This guidance and the sample code is now available as a Community Resource Kit and will eventually be incorporated into a future release of SCSF.
The resource kit also includes something a lot of people have been asking for – an example of programming against the manifest APIs in the Microsoft.Build.Tasks.Deployment.ManifestUtilities namespace. I wrote a Manifest Manager Utility as part of that effort and included in the download code that makes common tasks such as updating application files a lot easier. It takes care of signing both manifests at one to make sure they are in sync, updates the deployment manifest reference to the app manifest and other things like that. If you need to go beyond what it does, then you now have sample code available to show you how to work with the APIs.
Another thing included in the kit is an example server side deployment repository provider that allows you to take over the process of serving up manifests and application files on the deployment server so that you could retrieve them from anywhere or even generate some of the files on the fly.
Get it here!