There's a few ways to approach this, each with benefits and drawbacks.
- WMI: http://msdn.microsoft.com/en-us/library/aa547992.aspx The drawback is this is by Assembly, so you'd have to enumerate them first.
- BTSTask.exe: http://msdn.microsoft.com/en-us/library/aa559686.aspx Better, since it allows you to specify an Assembler or an Application. There's no object model, but executing from another program or script works fine.
- PowerShell Provider for BizTalk: http://psbiztalk.codeplex.com/ The way to go if you're scripting in PowerShell already.