He has been commemorated in a toast raised by College Wall on the eve of St Andrew's Day every year for over a century: "In Piam Memoriam J.K.S."

[5] In 1972, writer Michael Harrison claimed that a sexual relationship began between tutor and pupil, ending when Prince Eddy was gazetted to the 10th Hussars on 17 June 1885 and resulted in a scandal of which, apparently, little evidence remains.

[11] Those stanzas, in which Stephen deplores the state of contemporary writing,[12] appear in his poem 'To R. K.': Will there never come a season Which shall rid us from the curse Of a prose which knows no reason And an unmelodious verse: When the world shall cease to wonder At the genius of an Ass, And a boy's eccentric blunder Shall not bring success to pass:

"The Last Ride Together (From Her Point of View)" parodies Robert Browning's "Last Ride Together"; Lord Byron is parodied in "A Grievance"; and William Wordsworth in "A Sonnet": Two voices are there: one is of the deep; It learns the storm-cloud's thunderous melody, Now roars, now murmurs with the changing sea, Now bird-like pipes, now closes soft in sleep: And one is of an old half-witted sheep Which bleats articulate monotony, And indicates that two and one are three, That grass is green, lakes damp, and mountains steep: And, Wordsworth, both are thine.

Stephen was at Cambridge at the same time as the distinguished antiquarian and writer of ghost stories, M. R. James, and mentions him at the end of a curious Latin celebration of then-current worthies of 'Coll.

Stapleton's Eton School Lists 1853-1892, and the author refers to him in the preface as "an Etonian of great promise, who died only too early for his numerous friends".

[15][16] In January 1892, Stephen heard that his erstwhile pupil, the 28-year-old Prince Albert Victor, Duke of Clarence, had died of pneumonia at Sandringham, after contracting influenza.

Ever after, the King's Scholars of Eton College have honoured his memory with a toast at the Christmas Sock Supper and other festive occasions – in piam memoriam J.K.S.

Renewed interest in the 1888 Whitechapel murders had exploded in 1970 when British physician Thomas E. A. Stowell, allegedly working from the papers of Sir William Gull, made the veiled suggestion that Stephen's former pupil Prince Albert Victor, named only as "S", was the culprit.

[18] In 1972, writer Michael Harrison, working from this sensational theory, had come to the conclusion that "S" was not the prince, but actually Stephen who was committing the murders "out of a twisted desire for revenge" because of the dissolution of an alleged homosexual relationship between the two.

Harrison contends that the breakup of the relationship with Eddy, combined with his mental decline, provoked Stephen to act out his own poem "Air: Kaphoozelum", in which the protagonist kills 10 harlots.

[20] This and similar theories have been dismissed on a number of counts, with some citing that Stephen would have been unable to commit any murders in London and return to Cambridge in time for lectures the following morning.