Army and Battles
Alexander's army and generalship
Reader's Companion to Military History: Alexander the Great. Excellent long entry by Eugene N. Borza.
Good military biography of Alexander by Dennis Morehouse (Suite 101, General Military editor)
Amazon. The Generalship of Alexander the Great by J.F.C. Fuller. This is an interesting book. A British general, Fuller (1878-1966) was one of the architects of tank strategy and a well-considered historian in his later years. His book is interesting, and has something to contribute. That said, amateur historians probably give it more attention than it deserves, and it is not recommended as a general introduction to Alexander.
Pothos.org: Nick Wellman has written a number of lengthy treatments of military topics, including:
Arrian on Alexander's Major Battles from Chinnock's translation, excerpted by Dr. Nicholas Pappas, Sam Houston State University. Other selections from Arrian and Plutarch available here (search down).
Leaders and Battles Database: Alexander the Great. Entry by Kimberly J. Largent.
Alexander the Great: The Path to Deification by Dr. Evangellos Tzahos, a biographic article from Military Review, the official magazine of the Greek Army. Focuses on military aspects. Some erroneous information, e.g. the "royal newspapers."
Amazon. Alexander the Great and the Logistics of the Macedonian Army by Donald W. Engels. Engels' book produced something of an eclat in the field. For related books and reviews of Engels see Other Books.
"The Degradation of Alexander the Great's Motivational Tactics" by Nils Marthinsen (from Michael Arnush's course Alexander the Great). Good idea for a paper.
"Alexander's motivational tactics deteriorated over his career and led to the loss of control over his troops and subjects directly preceding his death. Whereas he once employed altruistic and genuine motivational tactics on his men early in his command, he gradually began using more sinister strategies on his kinsmen."
"An Ancient Coalition: The Composition of Alexander the Great's Army" by Micah Greenbaum (from Michael Arnush's course Alexander the Great).
The Army of Alexander the Great (Sander van Dorst)
Battle of Chaeronea
Reader's Companion to Military History: Chaeronea. Excellent long entry by Victor Davis Hanson.
Diodorus Siculus on the Battle of Chaeronea (338 B.C.), from the Ancient History Sourcebook.
Wikipedia: Battle of Chaeronea (338 BC). Minimal so far.
Battle of Granicus
Wikipedia: Battle of the Granicus. Usual Wikipedia caveats apply.
Battle of Issus
"Upset at Issus" by Harry J. Maihafer, Military History Magazine (October 2000), picked up by About.com. Lengthy.
Wikipedia: Battle of Issus. Usual Wikipedia caveats apply, but damn if this isn't a long entry! Busy busy busy.
Battle of Issus by "Jojo Nebuchadnezzar." Unsatisfactory, but highly-graphical hobby-report. Others in this collection include:
Siege of Tyre
History of Phoenicia, with a detailed account of Alexander and Phoenicia, especially the siege of Tyre.
Battle of Gaugamela
Reader's Companion to Military History: Battle of Gaugamela. Excellent long entry by Eugene N. Borza.
Wikipedia: Battle of Gaugamela. Usual Wikipedia caveats apply.
Web Archive: Gaugamela: "Dismantling the first world conqueror" (somewhat strange title) from the Ned Net.
"Alexander's Grand Tactics at Guagamela (sic): Prudence or Foolishness?" by Anatoly Ostrovsky (from Michael Arnush's course Alexander the Great). Ouch on the "sic." Unfortunately, Ostrovsky caries the spelling error through.
"The Battle of Arbela, B.C. 331" from Fifteen Decisive Battles of the World: From Marathon to Waterloo (1883?) by Edward Shepherd Creasy.
The Invasion of Afghanistan by Alexander from Afghanland.com.
"Alexander the Great's Most Heroic Moment" Peter G. Tsouras (Military History, June 2004), on Alexander's turning-back from the Hydaspes and"the most heroic moment"the action among the Mallians.
"Battle of the Hydaspes River" by Harry J. Maihafer (Military History, February 1989). Synthetic narrative, now somewhat dated.
Wikipedia: Battle of the Hydaspes River. Usual Wikipedia caveats apply.
Alexander's Invasion of India from "Political and Social Ethics of India" by Sanderson Beck.
Alexander's siege of Halicarnassus. Some info from Focus on Bodrum.
Amazon. Cavalry Operations in the Ancient Greek World by Robert E. Gaebel. Covers Alexander and the Hellenistic period.
Review by Kevin Carroll, H-Net.
"One very important development here was the use of a wedge formation of cavalry, which overcame the problem of charging an infantry force (for example, p. 158). Alexander improved on what Philip had done and gave the Greek world a cavalry that was a major component of military forces."
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Wiki Classical Dictionary, currently focused on Alexander