Is there a way to add a command-line switch to a program that runs from file associations?

For instance, I run a browser by clicking a link in a mail client. But I want that browser to always run with a command-line switch.

You can create a shortcut for the program you want to execute command line or open Properties page of the shortcut and from Shortcut tab you can add the command line you want to execute.

And how will I associate that shortcut with the file types?

For your specific case with the browser for running mail, since you're specifically using the browser, you can look into Browser Chooser 2, which I use to hand pick which browser opens which links that get passed to it as the default URL handler in Windows.

You can have as many items as you want, up to a width of 10 per row, and can have the same item more than once (i.e. Edge and another Edge for the same profile but with special parameters passed to it).

If you need help setting it up, let me know, I've been using it for years, and can probably help get you where you want to be with it.

If you're talking about a lot of different programs, though, i haven't actually tried to use BC2 for anything else other than URLs and web pages. Theoretically, it should work, since you can use the settings to add the application to the default apps list, and then assign it for numerous file types and protocols, but I don't know if Windows 11 will allow you to set it as default for protocols it hasn't actually registered itself as the handler for.

Check it out and see. May be what you're looking for.