Virtually everyone who has applied to Matasano has written a "cover letter" of some sort. The only ones who don't are clearly resume spammers. So the answer to your question is, from what I can tell, "everybody".
You're right that resumes are a crappy way to land a great job. To get a great job, pick 5 companies you desperately want to work for, ignore their job reqs, and track down the person inside each that runs the group that could hire you. Use your friends to help you do this, or to come up with ideas for companies to work for. Do not simply bounce around your network; that's a great way to lose 10 years of your life in mediocre roles. Notice how some of your friends have f'ing awesome gigs and some of them don't.
But: either do the resume/"job application" thing right, or don't bother doing it at all. Why waste your time? If the job is worth getting, it's worth playing the interview/negotiation game 100% perfectly.