* Header image that states "Joel On Software" and links to the homepage. This is a common website device. One
* Another text link before the article title. Ok, this one seems extraneous. Though since the first is an image, this is more SEO friendly. Two
* Not mentioned anywhere in the article.
* The footer contains another link. Again, this isn't really irregular. Three
* The email for the author of the article. Would it satisfy you if Joel had used another domain for his email address? Four
So there are a grand total of 4 appearances on that particular page, and with the exception (maybe) of one, none are spammy.
Did you come into this discussion solely to diss the author? Joel was pointing out something inane in a wizard dialog box, and you essentially call him a hypocrite.