Most companies grow gradually over the years, and keep finding new systems to meet specific business needs. This has resulted in a very diverse spread of software within organisations, which can be difficult to manage. With SharePoint 2007 and 2010, Microsoft is now able to meet a large number of these business needs, but not all of them.
In some cases, it makes sense to replace old systems with the newer Microsoft technology. In other cases, it makes more sense to use SharePoint as a front-end for more complex systems that should still be running in the background.