I don't do this often, so I'd be wary of reading in too much. In each case, I got an interview and one job, though that took awhile. (The hiring manager did not comment on the letter, but rather on the table at the top—probably because I couldn't find his name.)
I try to find the appropriate person to contact through LinkedIn, ideally a manager in the department of interest; I wrote to a (small) company president once, too. I try to avoid recruiters if I can help it, though my bias against them is perhaps a little uncharitable. The goals are two: to sidestep the usual application process through a little elbow grease and to differentiate myself in the candidate pool. I'm probably a pretty average programmer, and this has been a useful tool for me.
In the past, cover letters were usually a weak point because I would use boilerplate language that comes across as a bit canned. I've had the luxury lately of not having to do this: the letters were all written for companies I thought I really wanted to work for, so the interest was genuine and (hopefully) came across that way.
That’s a very interesting tactic.