On POSIX the interpreter will be read from the first line of a file.
On Windows the interpreter will be read from the Registry HKEY_CLASSES_ROOT\.<file-extension> .

So the correct way to associate a interpreter to a file is to invent a file-extension for every interpreter.
Like /usr/bin/python /usr/bin/python3 and /usr/bin/python3.1 on POSIX, there should be .py .py3 and .py31 on Windows!

I attached a example-registry-patch to register extensions for 2.5, 2.6 and 3.1 .
If you want to use it, you need to adjust the paths!

I propose to change all Python-Windows-installer to install versioned extensions.

If you want a switcher application, it should read the first line of the script and match it against ".*/python(.*)$". So the default POSIX "#!/usr/bin/python3.1" can be kept unchanged. With that rexex the app-path can be read from "HKEY_LOCAL_MACHINE\SOFTWARE\Python\PythonCore\<regex-match>\InstallPath\".

BTW.
It would be nice if Python would call itself "Python 3.1" instead of "python" in the "Open with..."-list! The current naming is problematic if you install more than one Python version.