There are many cartoons produced during the Golden Age that make allusions to science fiction elements: Hare Devil Hare, To Spring, Duck Dodgers in the 24th-and-a-Half Century, The Impatient Patient, the Fleischer Superman shorts, Cupid Gets His Man, The Sunshine Makers, The Cat That Hated People, and many more. A number of the aforementioned shorts appear on an old DVD I owned as a child, Cartoon Crazys: Sci-Fi. What confuses me about that particular collection was the inclusion of Prest-O Change-O and Cookin' with Gags, neither one of which appear to allude to anything science-related.

What other Sci-Fi shorts can you pinpoint? And what makes you believe they would fall into the realm of Sci-Fi?

"Popeye, the Ace of Space"
"Boo Moon"
"Destination Magoo"
"Woodpecker From Mars"
"Woodpecker in the Moon"
"Space Mouse" (Lantz-Hickory, Dickory and Doc)
"Switchen' Kitten"
"Mouse Into Space"
"Bomb Voyage" (The Inspector)

There was a "trilogy" of Chuck Jones Tom and Jerrys set in outer space:

"O Solar Meow"
"Guided Mouse-ile (or Science on a Wet Afternoon)"
"Advance and be Mechanized"

(Though all of these were directed by Chuck's animators, not by Chuck himself.)

Starting in the late 1950's Paramount Cartoon Studios really went over board with cartoons about aliens and outer space. The 1959 Noveltoon "Out of This Whirl" introduced Kozmo the Martian (and his magic ray gun), who appeared in 3 more cartoons: "The Kid From Mars", "Kozmo Goes To School" and Seymour Kneitel's final cartoon, "Space Kid". (Though the character's appearance was redesigned for these other 3 cartoons.) Other Paramount cartoons from the early 1960's include "Planet Mouseola" (with Skit and Skat, the replacements for Herman and Katnip), "Cape Kidnaveral" and "Galaxia".

And if you count the 1960's TV Popeyes:

"Hits and Missiles" (Seymour Kneitel's first TV Popeye)
"Incident at Missile City" (Seymour Kneitel)
"Robot Popeye" (Seymour Kneitel)
"There's No Space Like Home" (Gene Deitch)
"From Way Out" (Gene Deitch) ("I doesn't like juvenile delinquinks, no matter what planet they is from!")
"Astro Nut" (Gene Deitch)
"Have Time, Will Travel" (Gene Deitch)
"Intellectual Interlude" (bizarre cartoon in which scientists make Popeye a genius)
"Partial Post" (VERY bizarre cartoon with an alien that looks like a mailbox)
"The Ace of Space" (Larry Harmon)
"Childhood Daze" (Larry Harmon)
"Popeye the Popular Mechanic" (Jack Kinney) (Popeye builds a robot named Mac)

And there were 4 Jack Kinney Popeyes with Professor O. G. Wottasnozzle's time machine:

"Time Marches Backward"
"Invisible Popeye"
"Out of This World"
"The Black Knight"