The BizTalk 2006 version and API is 100% backwards compatible with the 2004 version and API. BizTalk 2006 is built against .NET2.0 while the BizTalk 2004 assemblies were built against .NET1.1. Although I’m not working for Microsoft this surely means that for the BizTalk 2006 version the Microsoft BizTalk product team has:
1. Checked the re-used BizTalk 2004 code parts against the new .NET version for incompatibilities and resolved all of them for the BizTalk 2006 release

2. Rewritten parts of the original BizTalk 2004 implementation in order to benefit from the new framework version (such as a performance gain) without breaking compatibility with the previous BizTalk version.

3. Added a lot of new BizTalk functionality written from scratch in .NET2.0 code.

In general .NET framework supports installing and running different framework versions side-by-side on a single machine. By default your custom old .NET1.1 applications will run with .NET2.0 when you run them on a machine with 2.0 installed. If you detect incompatibilities you can instruct .NET to load the old runtime version you originally built your application against (by means of configuration). Or you can choose to fix the incompatibility in your code and recompile for .NET2.0.

Whole different story for your newly written .NET2.0 applications: they only run with 2.0 or higher compatible version (for example 2.1). 

Microsoft BizTalk 2006 is a ‘new application’ and is ‘built against’ .NET 2.0 (beta) and as a consequence will only run with .NET framework 2.0 or higher compatible version. The BizTalk 2006 host instances will load and execute code using CLR .NET2.0 and as a consequence the assemblies it loads will execute within .NET 2.0. Your assemblies used inside orchestrations, your custom adapters and your pipeline components and their dependencies will all have to be compatible with .NET2.0. You don’t have the option to instruct to load the .NET framework version you built your assembly against because loading 2 different CLR versions in the same process is not supported. Here is a good post from Junfeng Zhang about the subject: The CLR Side by Side and Compatibility.

This means that as a BizTalk developer you should at least perform step 1 from the above steps for all your BizTalk 2004 custom code. If you’re lucky you detect no incompatibilities and it will work by default. But if you do detect incompatibilities then you’ll have to re-code and re-compile. For more information on the .NET CLR see Suzanne Cook’s weblog