This month I have had to lookup BizTalk 2006 behaviour for 64 bit architectures for two different clients. It doesn't seem to be well known, but this should be more of an issue in future.
Firstly, Microsoft documents BizTalk as supporting 64 bit, and then follows up with a few exclusions: ia64 bit for one, and many of your favorite adapters for another. http://technet.microsoft.com/en-us/library/aa560166.aspx.
So if you are going to target 64 bit architecture, be careful with your deployment design i.e. the host specifications. By default you will only have 32 bit hosts which run in a compatibility mode. You will have to create specific hosts for 64 bit support, otherwise your solution will likely run *slower* than on a 32 bit machine. Also, don't create too many host instances as this can pummel your message box(es). I recommend creating SendRcv host for each of 32 and 64 bit, then creating your Processing hosts as 64 bit. Be sure to check with vendors of 3rd party adapters to see if they are compatible.
In terms of installing your apps, you will not need to recompile .NET code. The installation is simlilar, but be aware that there is a second .net config file which you should be awaare of if you are using AppSettings in the normal one "btsNtSvc.exe.config" and "btsNtSvc64.exe.config". Also, if you are using DTD's then you will likely need to copy them to both system32 and WOW64 (depending on the adapter used).
For fun, I'll also mention clustering design. With BizTalk, the best way to cluster is to use the "Group" which means you install BizTalk on multiple servers and point them to the same Message box. You then simply declare a host instance for each server and you have automatic load-balancing clustering. Yay! The exception is that some adapters don't work well when you allow them to run multiple times. Here is MS on this issue: http://www.microsoft.com/technet/prodtechnol/biztalk/2006/library/bts06clustering/
The solution is to have a combination of Windows clustering configuration and also use a BizTalk group. Most items can run on multiple servers for good performance, and Adapters such as SQL Receive (schedule) and FTP Receive need to run in one instance of a Clustered host so they don't publish two copies of the same info.
-Jennifer Zouak