Most of them! Long form's great when it's pulled off correctly, but it's much harder to do right than a shorter song. Big offenders include In the Presence of Enemies, Anesthetize, The Poet and the Pendulum - which, compare and contrast to Blind Faith, Arriving Somewhere But Not Here, and Ghost Love Score. The latter selection are still long, anywhere from three to four times as big as the standard radio hit, but I think they feel more cohesive, less of a hodge-podge and more of a journey. They use the medium a lot better.
Not to say short songs can't be scattergun too, nor that epics are always less cohesive than their shorter counterparts, nor that being less cohesive is always bad! A Change of Seasons, though it's far from my favourite DT epic, is one of those songs where everything is very much part of the same story, and very definitely feels like it. I prefer Octavarium, but it's way more bipolar, as is something like Prophets of War, which completely loses momentum somewhere around the first chorus, or A Rite of Passage with its bafflingly abrupt instrumental section. But I think long songs, because they're so rare and mythical, are almost considered achievements unto themselves, like it's a sign of genius, whereas I think it's just as often the case that an epic's a sign that it would've been nice to parachute some kind of editor in at some point.
(A Rite of Passage, incidentally, could totally use an editor too. It's a short song masquerading as a long-ish song - I like it, but I reckon it could be as short as Supermassive Black Hole, and all the better for it.)