Migrating content with SharePoint is a well-known pain point. All too often, SharePoint just isn't up to the job of migrating everything you need, potentially leaving you with a broken and incomplete system. A common complaint from clients dealing with SharePoint is that out of the box, workflows are not usually migrated - the workflow definitions, workflow states, and workflow tasks are all missing.. Or that business critical content is suddenly missing... or functionality is broken..

Joel Olson has posted a blog entry where he's started collecting all the nasty details. What Doesn’t Migrate with SharePoint Built in Import/Export and other known issues. For example, "Object GUIDS are not preserved (This causes all sorts of weird things and can cause issues down the road. Empty folders may not migrate)."

Third party tools exist to assist with migration, but even they are limited in terms of completeness, and realistically it is often necessary to replicate SharePoint at the infrastructure level. Virtualisation makes this easier, as do various SAN options such as NetApp filers. For disaster recovery purposes a lot of work is usually required to identify everything that needs to be copied and their dependencies, and this needs to be considered for every patch or change made to the system. SharePoint out of the box is just not very resilient at facing different patch levels, database schemas, filesystem changes, or other configuration changes. 

Part of the product we're working on will help address this at the content layer, by letting you define business-critical information and ensure that it is replicated to an appropriate place automatically, and by providing a tool to ensure that your configuration meets your compliance and security baseline.

Good tools will help organizations save a lot of time and money in their SharePoint migrations, but proper procedures and testing will remain critical. If you are planning a SharePoint migration (whether 2010 or 2007), or if you have needs around disaster recovery or high available that require replication or migration of environments, you'll need to make sure that you think about how you handle SharePoint's limitations and issues, both up front and in an ongoing manner. Microsoft really need to do a better job addressing these issues, because the fears and problems that can arise will inhibit customers from adopting Microsoft's "latest and greatest" releases. Until this occurs - over the 5 year strategic timeframe - I don't think there is any real alternative for customers but to buy additional tools and ensure they have people experienced in SharePoint migrations.