Microsoft has three embedded operating systems, these are...
- Windows Embedded CE 6.0
- Windows XP Embedded SP2 (and Feature Pack 2007 coming soon)
- Windows Embedded for Point of Service
If you also include the .NET MicroFramework then that's four embedded operating systems. More information
I recently had MSDN TV turn up in my office and capture an interview where we talk about the differrences in the operating systems and also show the configure and build tools Windows Embedded CE 6.0.
Here's a link to the MSDN TV Video.