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MarkI love topics like this, and will weigh in with my (somewhat biased) opinion... I like to collect pennants, figural pieces, nodders, pins, etc, so I guess that must weigh into what a person considers "the best". For someone who collects books, photos, programs, cards and the like, the basis for an opinion could be completely different.
But in terms of the "visual" stuff, I completely agree with Mike, that the Athletics probably lead the pack, with Tigers and Cubs also being very strong. I would also throw the Indians and Dodgers in there. Chief Wahoo and the Bum are both classic images, though nowadays not "politcally correct". The Cardinals also deserve mention, as some of their pieces are just gorgeous.
As a Reds fan, I would place Cincy about in the middle. I did not like it when they "cheapened" the baseball-headed mascot in 1970. They even got rid of his moustache when they adopted Bob Howsam's "no facial hair" policy! And btw... Mr. Met is just a blatant copy 
I would rank the Senators and Phillies at the bottom.
I do have a theory on why some teams continually produced better quality memorabilia than others... Animal or cartoonish character mascots (see all mentioned above) are more condusiive to artistry and creativity. They make for interesting figural pieces, banks, statues, pennants, logos, etc. How much can you really do, to depict a "Senator" or a "Phillie" (or in modern terms, a Rockie, Mariner, Ranger, or Astro?)