The InfoPath Team blog posted a series on how to programmatically extract/manipulate/combine an InfoPath Template (XSN) file. The example was about changing your website URL, however, I'm sure images of auto-generated templates are dancing around your head as they are mine. (“Hey, it's just XML”, he said.)
Unfortunately their solution relies on running the CAB utilities, extract.exe, etc. The Microsoft Cabinet SDK also has cabinet.dll to allow programmatic access to CAB files. This October 2004 Dev Source article explains how to create a managed wrapper around the Cabinet API.
Someone in the blogosphere pointed me to this excellent series from June 2003 that explains the .NET XML APIs and provides guidelines on when to use each. Written by Aaron Skonnard himself. Highly recommended.
Note that this will be dated material when .NET 2.0 is released.
Christian Weyer's company thinktecture is offering the WSCF toolkit to make practical XSD-driven contract first web service programming.
Benjamin Mitchell has a great description of the tool. More here by Simon Guest.
Mention is also given here by Arron Skonnard.
The object generation portion of WSCF competes with the xsd.exe and XSDObjectGen tools.