Feel free to shoot me down here, but how about the following:

[[ include: Foo.fountain]]

As I see it, the advantages of dropping the # and appending a : are:

• "It's cleaner" -- Justin Timberlake
• It conforms more with the YAML-style metadata/title-page frontmatter
• If the include does not resolve to a file, they can be parsed as a regular note and still make sense, e.g.

[[ include: that part where she goes back for the dog.. ]]

• ...but it's more likely a writer will write, which will be ignored:

[[ include that idea with the monkey butler stealing the martini ]]

Thoughts?