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I have a source base that, depending on defined flags at build time, creates two different apps. I can build both of these apps using a Makefile by specifying two different targets, one that compiles with a flag and one that compiles without, and having an aggregate target that builds both.
How do I do the equivalent thing from Visual C# Express on Windows?
Create one solution with two project files in the same folder. Set two different configurations in your solution, one of them building one of the projects, the other one building the other project.
Alternatively, you can have one project which always builds to intermediate binary and then have a postbuild step that copies it to the final binary depending on the flag.