First, here's an off the top of my head answer I gave on rec.arts.sf.written (gosh how I miss that community in its Golden Age!) in December 1999. The original question was "Ten Best Novelettes" (by which the poster (Jerry Friedman) meant "long stories" -- roughly speaking, novelettes and novellas.) Naturally I added short stories too.
Here's what I posted.
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Here's my list, which extends to 12 authors and 14 stories (so sue me!):
(I've put it in my best guess at chronological order of publication)
"... and Now the News" by Theodore Sturgeon
"The Dead Past" by Isaac Asimov
"Flowers for Algernon" by Daniel Keyes
"The Sources of the Nile" by Avram Davidson
"Starfog" by Poul Anderson
"Nine Lives" and "The Stars Below" by Ursula K. Le Guin
"The Second Inquisition" by Joanna Russ
"Green Mars" by Kim Stanley Robinson
"The Last of the Winnebagos" and "Fire Watch" by Connie Willis
"The Originist" by Orson Scott Card
"Wang's Carpets" by Greg Egan
"The Ziggurat" by Gene Wolfe
"The Dead Past" by Isaac Asimov
"Flowers for Algernon" by Daniel Keyes
"The Sources of the Nile" by Avram Davidson
"Starfog" by Poul Anderson
"Nine Lives" and "The Stars Below" by Ursula K. Le Guin
"The Second Inquisition" by Joanna Russ
"Green Mars" by Kim Stanley Robinson
"The Last of the Winnebagos" and "Fire Watch" by Connie Willis
"The Originist" by Orson Scott Card
"Wang's Carpets" by Greg Egan
"The Ziggurat" by Gene Wolfe
And a list for short stories (10 authors, 12 stories):
"Scanners Live in Vain" by Cordwainer Smith
"Fondly Fahrenheit" by Alfred Bester
"The Man Who Came Early" by Poul Anderson
"The Man Who Lost the Sea" by "A Saucer of Loneliness" by Theodore
Sturgeon
"A Rose for Ecclesiastes" by Roger Zelazny
"Light of Other Days" by Bob Shaw
"The Milk of Paradise" and "The Last Flight of Dr. Ain" by James
Tiptree, Jr.
"The Marvelous Brass Chess-Playing Automaton" by Gene Wolfe
"Out of All them Bright Stars" by Nancy Kress
"New Rose Hotel" by William Gibson
"Fondly Fahrenheit" by Alfred Bester
"The Man Who Came Early" by Poul Anderson
"The Man Who Lost the Sea" by "A Saucer of Loneliness" by Theodore
Sturgeon
"A Rose for Ecclesiastes" by Roger Zelazny
"Light of Other Days" by Bob Shaw
"The Milk of Paradise" and "The Last Flight of Dr. Ain" by James
Tiptree, Jr.
"The Marvelous Brass Chess-Playing Automaton" by Gene Wolfe
"Out of All them Bright Stars" by Nancy Kress
"New Rose Hotel" by William Gibson
Oh, and a list of honorable mentions (this is so hard!): "The Star" by Clarke, "Nobody's Home" by Russ, "Rat" and "Think Like a Dinosaur" by James Patrick Kelly, "E for Effort" by T. L. Sherred, "The Star Pit" by Samuel R. Delany, "Imaginary Countries" and "Winter's King" by Ursula K. Le Guin, "The Moon Moth" by Jack Vance, "Wall of Crystal, Eye of Night" by Budrys, "The Crystal Spheres" by Brin, "The Other Dead Man" and "How the Whip Came Back" and "Seven American Nights" and etc. by Wolfe, "The Only Neat Thing to Do" and "And I Awoke and Found Me Here on the Cold Hill's Side" and etc. by Tiptree, "Why I Left Harry's All-night Hamburgers" by Watt-Evans, "Starship Day" by Ian R. MacLeod, "Bloodchild" by Octavia Butler, "All My Darling Daughters" and "At the Rialto" and "Schwarzchild Radius" by Willis, "Stairs" by Neal Barrett, Jr., "Great Work of Time" by John Crowley, "An Infinite Summer" by Christopher Priest, "Inconstant Moon" by Larry Niven.
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And for the Locus All Centuries Poll, here's my submission, from 2012 for stuff through 2010:
The Locus All Centuries Poll -- best SF/Fantasy novels and short fiction of the 20th and 21st centuries (separately) is ending just about now. Here's my votes (note that they change over time, and the order is random, and there are stories I missed!)
20th Century Novella:
1: "Story of Your Life", Ted Chiang
2: "Great Work of Time", John Crowley
3: "Green Mars", Kim Stanley Robinson
4: "The Blabber", Vernor Vinge
5: "Seven American Nights", Gene Wolfe
6: "The Star Pit", Samuel R. Delany
7: "The Last of the Winnebagos", Connie Willis
8: "E for Effort", T. L. Sherred
9: "The Originist", Orson Scott Card
10: "The Gold at the Starbow's End", Frederik Pohl
20th Century Novelette:
1: "Wang's Carpets", Greg Egan
2: "Fondly Fahrenheit", Alfred Bester
3: "The Second Inquisition", Joanna Russ
4: "The Sources of the Nile", Avram Davidson
5: "A Rose for Ecclesiastes", Roger Zelazny
6: "Starfog", Poul Anderson
7: "An Infinite Summer", Christopher Priest
8: "Nine Lives", Ursula K. Le Guin
9: "The Stars Below", Ursula K. Le Guin
10: "Tlon, Uqbar, Orbis Tertius", Jorge Luis Borges
20th Century Short Story:
1: "Out of All Them Bright Stars", Nancy Kress
2: "The Man Who Lost the Sea", Theodore Sturgeon
3: "The Milk of Paradise", James Tiptree, Jr.
4: "Nobody's Home", Joanna Russ
5: "Light of Other Days", Bob Shaw
6: "Day Million", Frederik Pohl
7: "New Rose Hotel", William Gibson
8: "The Last Flight of Dr. Ain", James Tiptree, Jr.
9: "The Man Who Came Early", Poul Anderson
10: "Schwartz Between the Galaxies", Robert Silverberg
21st Century SF Novel:
1: Cloud Atlas, David Mitchell
2: The Yiddish Policemen's Union, Michael Chabon
3: The Sky So Big and Black, John Barnes
4: Spin, Robert Charles Wilson
5: Ares Express, Ian McDonald
21st Century Fantasy Novel:
1: Jonathan Strange and Mr Norrell, Susannah Clarke
2: Lavinia, Ursula K. Le Guin
3: The Light Ages, Ian R. MacLeod
4: The Name of the Wind, Patrick Rothfuss
5: The City and the City, China Mieville
21st Century Novella:
1: "New Light on the Drake Equation", Ian R. MacLeod
2: "Magic for Beginners", Kelly Link
3: "A Billion Eves", Robert Reed
4: "The Engines of Desire", William Barton
5: "The Tear", Ian McDonald
21st Century Novelette:
1: "The Voluntary State", Christopher Rowe
2: "The People of Sand and Slag", Paolo Bacigalupi
3: "Lull", Kelly Link
4: "The Path of the Transgressor", by Tom Purdom
5: "Finisterra", by David Moles
21st Century Short Story:
1: "The House Beyond Your Sky", Benjamin Rosenbaum
2: "Three Days of Rain", Holly Phillips
3: "Pip and the Fairies", Theodora Goss
4: "More Adventures on Other Planets", Michael Cassutt
5: "Exhalation", Ted Chiang
20th Century Novella:
1: "Story of Your Life", Ted Chiang
2: "Great Work of Time", John Crowley
3: "Green Mars", Kim Stanley Robinson
4: "The Blabber", Vernor Vinge
5: "Seven American Nights", Gene Wolfe
6: "The Star Pit", Samuel R. Delany
7: "The Last of the Winnebagos", Connie Willis
8: "E for Effort", T. L. Sherred
9: "The Originist", Orson Scott Card
10: "The Gold at the Starbow's End", Frederik Pohl
20th Century Novelette:
1: "Wang's Carpets", Greg Egan
2: "Fondly Fahrenheit", Alfred Bester
3: "The Second Inquisition", Joanna Russ
4: "The Sources of the Nile", Avram Davidson
5: "A Rose for Ecclesiastes", Roger Zelazny
6: "Starfog", Poul Anderson
7: "An Infinite Summer", Christopher Priest
8: "Nine Lives", Ursula K. Le Guin
9: "The Stars Below", Ursula K. Le Guin
10: "Tlon, Uqbar, Orbis Tertius", Jorge Luis Borges
20th Century Short Story:
1: "Out of All Them Bright Stars", Nancy Kress
2: "The Man Who Lost the Sea", Theodore Sturgeon
3: "The Milk of Paradise", James Tiptree, Jr.
4: "Nobody's Home", Joanna Russ
5: "Light of Other Days", Bob Shaw
6: "Day Million", Frederik Pohl
7: "New Rose Hotel", William Gibson
8: "The Last Flight of Dr. Ain", James Tiptree, Jr.
9: "The Man Who Came Early", Poul Anderson
10: "Schwartz Between the Galaxies", Robert Silverberg
21st Century SF Novel:
1: Cloud Atlas, David Mitchell
2: The Yiddish Policemen's Union, Michael Chabon
3: The Sky So Big and Black, John Barnes
4: Spin, Robert Charles Wilson
5: Ares Express, Ian McDonald
21st Century Fantasy Novel:
1: Jonathan Strange and Mr Norrell, Susannah Clarke
2: Lavinia, Ursula K. Le Guin
3: The Light Ages, Ian R. MacLeod
4: The Name of the Wind, Patrick Rothfuss
5: The City and the City, China Mieville
21st Century Novella:
1: "New Light on the Drake Equation", Ian R. MacLeod
2: "Magic for Beginners", Kelly Link
3: "A Billion Eves", Robert Reed
4: "The Engines of Desire", William Barton
5: "The Tear", Ian McDonald
21st Century Novelette:
1: "The Voluntary State", Christopher Rowe
2: "The People of Sand and Slag", Paolo Bacigalupi
3: "Lull", Kelly Link
4: "The Path of the Transgressor", by Tom Purdom
5: "Finisterra", by David Moles
21st Century Short Story:
1: "The House Beyond Your Sky", Benjamin Rosenbaum
2: "Three Days of Rain", Holly Phillips
3: "Pip and the Fairies", Theodora Goss
4: "More Adventures on Other Planets", Michael Cassutt
5: "Exhalation", Ted Chiang