BizTalk Server 2006 allows us to use the concept of Application to logically organize the artifacts in our solutions, such as orchestrations, schemas, send and receive ports, etc. Further, you can add references from one application to other applications, which allows you - for example - to bind an orchestration logical receive port to a receive port defined in some other (referenced) application, or create a Send Port filter using a property defined in a Property Schema included in other application.
You can use the Administration Console to add these references manually, by simply selecting an Application's properties and the "References" tab.
I am a huge fan of scripts and automation, so I quickly developed a command line tool to help me a) create applications and b) add references from one application to other application, which I use further automate my deployments, which sometimes are not easily done with MSI's.
Sample usage is:
BizAppManage -AddApp nameOfAppToCreate nameOfAppToReference1 nameOfAppToReference2 nameOfAppToReference3
BizAppManage -AddRef nameOfExistingApp nameOfAppToReference1 nameOfAppToReference2
I've used Carlos Medina's BtsHelper class to avoid hard-wiring the BizTalk connection string.