So, where does the phrase actually come from? Well, as best as Google can tell me:
GREAT MINDS THINK ALIKE -- "Often quoted in jest today, this saying originated in the seventeenth century as the comic-sounding 'Great wits jump.' Daubridgecourt Belchier first recorded the saying in 'Hans Beer-Pot' (1618) as 'Good wits doe iumpe (agree).'...The expression 'Great minds jump' appeared in the late 1800s..." From "Wise Words and Wives' Tales: The Origins, Meanings and Time-Honored Wisdom of Proverbs and Folk Sayings Olde and New" by Stuart Flexner and Doris Flexner (Avon Books, New York, 1993).and also:
Used ironically. Both verb and noun have changed in the course of this proverb's history, the earliest instance of the present form thus far discovered being quot. 1898. Jump used absolutely in the sense of ‘agree completely’ or ‘coincide’ is now archaic.Though he made that verse, Those words were made before. ‥Good wits doe iumpe.
[1618 D. Belchier Hans Beer-Pot D1]Great wits jump: for the moment Dr. Slop cast his eyes upon his bag‥the very same thought occurred.
[1761 Sterne Tristram Shandy III. ix.]As great minds jump this proves‥that my Mind is Great!
[1889 A. James Journal 1 Dec. (1964) 61]Curious how great minds think alike. My pupil wrote me the same explanation about his non-appearance. ‥
[1898 C. G. Robertson Voces Academicae 24]‘Great minds think alike—that's why we're never in agreement.’
[2002 Washington Times 28 May C9 (Bottomliners cartoon)]
I probably wasted too much time thinking about the phrase and looking up its origins. But then again, I rarely have the time to just pursue such idles. I'm still glad I wasted some time satisfying an academic curiosity.