After giving it some thought, I've found a few things I would switch around in Mr. Spurgeon's list, as he suggests toward the end of the article. Most of what I would add has been covered in detail by other contributors (Eisner, 2000 AD, EC horror comics), but there are still a few worth adding, I think.
1. At least one Jim Woodring book or comic.
Woodring's best work, like Frank, takes the unsettling undercurrents in classic newspaper comics and cartoons and hauls them screaming up to the surface- I promise you you'll never read Krazy Kat the same way again. A major artist who has more than earned a place in the critical canon. And we wouldn't have Jerkcity without him.
2. A healthy collection of bande dessinee or other European graphic albums. This is sort of already covered by #10, "Several Tintin Albums" and #36, "A Few Comics Not In Your Native Tongue," but this is such a fertile area of comics that it deserves a wider, more inclusive category for the likes of Enki Bilal, Asterix, Moebius, Hugo Pratt, etc.
3. At least one art book by or critical examination of an artist or creator. There's been a flood of high-quality books of this type lately, from Mark Evanier's Kirby book to Paul Pope's PulpHope collection to the new Ditko book from Fantagraphics.
4. A complete run of Flex Mentallo.
2. A Complete Run Of Arcade
Too expensive to put together, and many of the major artists are represented elsewhere in the list.
21. One Run of A Comic Strip That You Yourself Have Clipped
Because most newspaper comics just aren't worth the effort anymore.
42. A Run Of Yummy Fur
Like Arcade, this is pretty expensive/difficult to put together, excellent though it is.
49. An Editorial Cartoonist's Collection or Two
I'll admit, I can't really justify this beyond some vague hand-waving about how single-panel cartoons with clearly labeled ideas aren't really all that relevant to modern comics and how they can be (and often are) crude and obvious, but this is personal taste more than anything.