Maybe he or a friend should submit the cover letter and his story to the business press. Wouldn't they be interested in something like that (as a job-hunting innovation)?
I couldn't think of the best way to do it: a very short cover letter basically saying "open that webpage to see my real cover letter" might just annoy the recipient; a somewhat regular cover letter (my choice then) with an invitation to open a link still needs to be distinctive enough to convince the recipient to click the link.
Oh, and the "design". Humongous blank space on the left; comic pushed off to the right. I really hope he didn't send it like that.
The problem I see is that he seems to be angling less for the job as a designer and more for Gabe and Tycho's (wait, are those their real names?) job as a cartoonist. One might worry that he'd have to be repeatedly told "No, sit down and fix the website, stop pitching us strip ideas"
I found a copy of the original job ad, btw:
http://www.be-mag.com/msgboard/showthread.php?18856-Penny-Ar...