We discussed global vs. file modules when covering projects and recommended using file based modules and not polluting the global namespace.
Nevertheless it is convenient to have some files just with type declarations (for smaller projects preferably one called globals.d.ts) in the global namespace to make it easy to have some types just magically available for consumption in all your TypeScript code. For any code that is going to generate JavaScript we still recommend using file modules.
globals.d.ts is great for adding extensions to lib.d.ts.