I'd usually rather have one very long flight and one shorter flight. Getting off a 7-hour flight and knowing I have another 7-hour flight just ahead is daunting (unless there's a half-day in between -- see below). But with a 3- and an 11-hour flight I can be productive on the 3 and really get into that delightfully mindless, nice-to-get-away-from-everything zone on the 11.
But it's more complicated: If traveling solo and the connection is 4 hours or less, I'd rather have the short flight closer to home (first on the outbound and last on the inbound). When headed on vacation I want to get off the long flight and start exploring something. When headed home I then get the short flight for one last catch-up on alone time before getting back to things at home.
If traveling solo and the connection can be scheduled long, though, I'd rather have two 7-hour overnight flights with 12-15 hours in between to explore a city.
If traveling with someone else, I'd rather have the short flight first in both directions. On the outbound the same reason applies. On the inbound I think most people I travel with don't want to get on another flight, even a short one, after a very long one. And I don't think they'd want two overnights in a row, either.
Seth