I have a help project that has two .NET assemblies. One is the main product assembly, and the other is a common assembly used by multiple products.

 The TOC is OK, except that it wants to use the common assembly Introduction topic as the one to open. I suspect it's because that file name is alphabetically first, because the product assembly is listed first on the Included Modules page.

How can I select which of the two projects the TOC opens with?

I would suggest creating a .html manually that is an introduction to the documentation set, then add that to the additional files and create an entry to point to that file as the first in the TOC.

If you are using HelpStudio, you can do that in there.