Exchange 5.5 does not integrate with the NT4 domain or the 
Windows 2000/2003 Active Directory in a meaningful way. A 
single user could be associated with several different 
mailboxes. Exchange 2000/2003/2007 integrates tightly with 
Active Directory, and there is a 1:1 relationship between 
mailboxes and AD user accounts. 
There are other differences, depending on whether you have 
a standard or enterprise version as it relates to maximum 
database size, but the directory integration is probably 
the biggest difference.

The primary differences are...
-Exchange 2000/2003 does not have its own directory or 
directory service; it uses Active Directory instead.
-Exchange 2000/2003 uses native components of Windows 2000 
(namely, IIS and its SMTP, NNTP, W3SVC and other 
components, Kerberos and others) for many core functions.
-SMTP is now a full peer to RPC, and is it the default 
transport protocol between Exchange 2000/2003 servers.
-Exchange 2000/2003 supports Active/Active clustering and 
was recently certified for Windows 2000 Datacenter/2003.
-Exchange 2000/2003 scales much higher.
-It boasts conferencing services and instant messaging.