For differences between 2004 and 2006 check out this site
[url]http://www.microsoft.com/biztalk/2006/prodinfo/whatsnew.mspx[/url]
[quote:05c311e3ac]Seamless upgrade experience. Upgrading from BizTalk Server 2004 to BizTalk Server 2006 is an in-place upgrade process. When a customer executes the BizTalk Server 2006 setup on a computer where BizTalk Server 2004 is already installed, the setup program will automatically upgrade the installation to BizTalk Server 2006. All solutions built for this earlier version will work unchanged in the new version.[/quote:05c311e3ac]
You can however rebuild all your solutions using VS2005 and redeploy. When you open a Biztalk 2004 project in VS2005 it will automatically upgrade the project.
Any adapters or pipeline components will continue to work, again you can rebuild in VS2005 if you wish to take advantage of .NET 2.0 features.