There are several different answers here. I think Zekestrom is right on the money with SF6. that one was also my first, so it holds a certain amount of personal nostalgia as well. I would also put SF7 as a close second.
But if you take away all of the intangibles and just look at it from a pure lineup standpoint, factoring in not only the films, but the order and pacing, two of the best lineups were one's I was unable to attend.
My runner up would be SF18:The Incredible Shrinking Marathon.
THE INCREDIBLE SHRINKING MAN
THE IRON GIANT
PLANET OF THE APES
TOP OF THE FOOD CHAIN (Premiere)
FREQUENCY (Premiere)
TRON
X
DEATH RACE 2000
MEN IN BLACK
THE FIFTH ELEMENT
FANTASTIC VOYAGE
Solid, something for everyone, great placement.
I implore anyone to come up with a better argument for the best marathon lineup (taking away any personal bias) than the aforementioned
NIGHT OF THE LIVING DREXEL 1993:
THE SHINING
A CHINESE GHOST STORY
NIGHT OF THE LIVING DEAD (1968)
The U.S. PREMIERE of RETURN OF THE LIVING DEAD 3
THE EXORCIST
The SECOND U.S. SCREENING of CRONOS
The MIDWEST PREMIERE of CARNOSAUR
EVIL DEAD 2
ARMY OF DARKNESS
HALLOWEEN
The MIDWEST PREMIERE of TICKS
THE TEXAS CHAINSAW MASSACRE
Anyone have a better argument? Or should the question really be "Okay, what is the second best Marathon lineup?"
On a side note, the marathons for me have always been about the little things as well, just like the moral of the fantastic film STRANGER THAN FICTION. The standing ovation for the live musical accompaniment, Gamera pushes Trekkie, hearing "aarrrrrr!" throughout the one with ESCAPE FROM NY, when the audience is quiet and respectful in all the right places, looking at the program and wondering what the hell is this movie from New Zealand called BRAINDEAD? Never heard of it, I wonder what it's about. Anyway, you get the idea.