Marty Wasznicky and Scott Zimmerman wrote an article in MSDN, where they lined out a couple tips and tricks for programming in BizTalk (best practices).
In the article they write about:
· Always Use Multi-Part Message Types;
· Always Try to Design Orchestrations with Direct-Bound Ports;
· Always Use Separate Internal and External Schemas;
· Never Expose Your Internal Schemas Directly in WSDL;
· Always Optimize the BizTalk Registry for Web Services;
· Always Set the Assembly Key File with a Relative Path;
· Never Overlook Free Sample Code;
· Debug XSLT in Visual Studio.
Besides best practices for programming there is also a BizTalk Server Best Practices Analyzer to use for deployment of the product in high availability, security, management and performance scenarios. There also logging possibilities for BizTalk to use log4net, see Scott Colestock’s blog for this. One can also generate a CHM file containing summaries of all your BizTalk artifacts (and relationships), plus business rules, plus port configurations, plus orchestration image snapshots using BizTalk Documenter. Finally there are some books about BizTalk, which I posted previously from APRESS.
To be professional active in developing BizTalk solution or setting up architecture for BizTalk solutions there is a lot of material and tooling out there to use. I have gained experience in using all these tools besides reading books, articles and so on. The article written by authors is another one that should be read and is a good addition to all information that is already published.
I would recommend all tools mentioned here if you not already know them or familiar with them. I refer to them together with the article so one can be on their way to create great solid BizTalk solutions.
Technorati: 
BizTalk Server 2006 
Marty Wasznicky 
BBPA 
Scott Colestock 
APRESS
