On the anniversary of Alexander the Great's death, N. S. Gill (ancienthistory.about.com) points to a couple of articles that go through some possibilities...Notably: Swine flu?* West Nile virus? Arsenic seems not quite up-to-the-moment...
Might I suggest: Knowing that a 72-foot statue of him would one day be erected in Skopje did him in? No, I imagine he would receive a tribute of such adulation pretty willingly.
*Ok, ok, the article doesn't really suggest H1N1, only generic influenza.