From Wikipedia, this statement tells the whole story:
Windows Embedded Enterprise brand of Windows Embedded Operating
Systems consist of Windows XP for Embedded Systems and Windows Vista
for Embedded Systems, which are the same versions of the OSes as are
available in retail but are licensed exclusively for use in embedded
devices. They are available for both x86 as well as x86-64 (x64)
processors.
Further confusing this branding decision, the only versions of Windows Vista available under Windows Embedded Enterprise are Business and Ultimate. In non-terse Microspeak, Windows Vista Business for Embedded Systems and Windows Vista Ultimate for Embedded Systems are both Windows Embedded Enterprise products.
Since you're effectively getting the exact same OS, the only benefits to choosing this product over any other version of Windows Vista are your desired licensing. Here's the comparison matrix of Vista products by edition, and as before, you're looking at the columns labeled Business and Ultimate, not Enterprise.
For versions of Windows that have actual tangible benefits in the form of smaller kernels and increased robustness for embedded systems, consider the remaining editions listed on this page.
For the benefit of current users at the time of this writing, this branding decision extends to Windows 7.
Here's the comparison matrix detailing the benefits of Windows 7 Professional SP1 and Ultimate for Embedded Systems. As before, Microsoft's product marketing is somewhat misleading:
These products are fully functional versions of Microsoft’s desktop
operating system intended for use in an embedded solution consisting
of purpose-built hardware and application software.
Here's the comparison of editions. You're looking at the columns labeled Professional and Ultimate again for the features you'll receive with either product offering.
For embedded solutions in Windows 7 that actually involve a customized version of the OS, consider Windows Embedded Standard or Windows Thin PC for slimming down aspects of the OS. Microsoft's documentation is far better than I can tractably fit in an answer here.