dearestwatson:

Watson’s middle initial appears only three times: here, at the foot of the sketch plan illustrating “The Priory School” (in the Strand Magazine in February 1904), and on the title page of A Study in Scarlet. Dorothy L. Sayers, in her classic article “Dr. Watson’s Christian Name,” argues that the “H” stands for “Hamish,” a Scotch name equivalent to “James” (see “The Man with the Twisted Lip” for an instance in which Watson’s wife refers to him as “James”). Several others propose “Henry,” primarily because of the high contemporary regard for cleric John Henry Newman. Still others, for varied but ultimately unconvincing reasons, propose “Hampton,” “Harrington,” “Hector,” “Horatio,” “Hubert,” and “Huffham.” One wag even suggests “Holmes”! 

John H. Watson is short for John Holmes-Watson is my new favourite theory