I am off to St. Louis next week to start another SharePoint project. I have become known in our group here at Microsoft for these types of projects because we “bend” SharePoint in a way that it was not designed out of the box. A lot of customers are using SharePoint to write WebParts for their applications, and use very few of the “real” SharePoint functionality. Visual Studio 2005 lets WebParts go native, but if you want to do something right now, you need to use SharePoint WSS or SPS. Although we don’t overstep any supportability boundaries, using SharePoint and having to move code such as pages and WebParts is not what SharePoint was designed to do.
Dan Larson has a great site that goes into more details about these challenges and actually supplies source code to build utilities that let you extract and restore individual document libraries and object within SharePoint. There are third party apps that can do this, but they are usually around backup and restore, where Dan’s stuff is more for development and is callable from a command line so I can wrap it with deployment scripts.