I’m big on outlining. It’s a great way to make sure that everything in your paper fits together and works toward the same goal. If you have stray elements, things that don’t really contribute toward your argument, they’ll really show up on an outline.
So, I think the first step of writing a good research paper is putting together your outline.
It can also be very effective as one of the last steps.
Here’s an interesting article on reverse-outlining: going back over your paper and outlining it as you’ve actually written it. It’s amazing how far your first draft can slip away from your original outline. So, reverse-outlining is a tool you can use to see if your argument still hangs together and if every section/paragraph still works toward that end. It can take a little time, but it’s well worth the effort.