Rubs hands. Are you ready Yellow and Peteneras? 
Differences:
Size: 800 versus 1300
Location: grimey London versus touristy Windsor - both have flight noise!
Academic Selectivity: Eton more academically selective but Harrow more oversubscribed and most boys need to be a "package" so in theory it's harder to get into.
Harrow has a fiercely loyal network which prioritizes old boys sons and offers work experience to current pupils. Harrovians are known to be very arrogant!
Eton has better facilities, grounds and societies.
I think the reasons one school is chosen over another by first time buyers or no connection to the schools would include:
One is more famous which is seen as pro or con
One is academically more selective
Location
Advice by prep Headmaster. Four Headmasters shrieked, "NO" when I suggested Harrow for very bright, unassumming son.
Just don't be the twit that stood up at the Harrow open day and asked why he should choose Harrow over Eton.
Well, Harrow and Eton choose you so if he did the same at Eton he wouldn't have the choice of either!