This list is from 1980, and I wouldn't entire agree with it myself (even for stories before that date), but it's a strong list, so I figured I'd post it. Malzberg's version, in the essay "The Cutting Edge" in The Engines of the Night (and then reprinted in the new expanded version, Breakfast in the Ruins), also has his explanations.
- "Vintage Season" by C.L. Moore
- "Her Smoke Rose Up Forever" by James Tiptree, Jr.
- "Particle Theory" by Edward Bryant
- "The Terminal Beach" by J.G. Ballard
- "Private Eye" by Henry Kuttner and C.L. Moore
- "Sundance" by Robert Silverberg
- "Anachron" by Damon Knight
- "The Men Who Murdered Mohammed" by Alfred Bester
- "Fondly Fahrenheit" by Alfred Bester
- "E For Effort" by T.L. Sherred
But I completely agree with Malzberg on "Fondly Fahrenheit;" he quotes Silverberg as calling it the single finest short story ever to come from science fiction, and I'd even go further: it's one of the very best stories ever written by an American, period.
I won't do my own list now, but, after mulling it over for a while on the bus, I think my list would have Walter Jon Williams's "Dinosaurs," Bruce Sterling's "We See Things Differently," and Greg Egan's "Learning To Be Me." (And maybe David Marusek's "We Were Out of Our Minds With Joy." And maybe Ted Chiang's "Hell Is the Absence of God." But I'd really have to poke through books to jog my memory of stories from before 1990, before doing a list, to be fair.)