What are the differences between ISA 2004 and ISA 2006?

Since ISA Server2006 is built on ISA Server2004 so it includes all features of ISA2004 Server plus some useful features including OWA and share Point publishing, better resistance against DOS attack, IPS/IDS, QOS and http compression. Further ISA Server2006 also supports form based authentication for publishing, a cool feature you find in later version.  

Share point Portal Server Publishing wizard .
Fully support for Exchange Server2007.
branch office VPN connetivity Wizard .
Flood Resiliency (ISA Server stop unavailable from flooding attacks ).
Enhanced remediation during attack.
Support for LDAP authentication (ISA Server2006 can access the Authenticate to Active Directory without being the member of the domain.
) BITS caching.(ISA Server2006 provides the caching mechanism for data received through BITS.
Any cache rule that you create can be enabled to cache BITS data.) Web Publishing load balancing .(Automatically balance request stream among ISA servers on the arry ) HTTP compression.(HTTP compression reduces file size by using algorithms to eliminate redundant data during transmission of HTTP packets) Quality of Service (new packet prioritization functionality (provided by the Diffserv Web filter), which scans the URL or domain and assigns a packet priority using Diffserv bits.) I hope it was helpful, vote if it is