Filmation's Superboy adventures were brief, only 34 six-minute episodes made over four years, as part of three different programs - The New Adventures of Superman, The Superman/Aquaman Hour of Adventure, and The Batman/Superman Hour - doomed not to be released on DVD on account of the legal dispute over Superboy between the Siegel estate and DC Comics. Very few can still be found on YouTube.
Our boy Krypto was featured in all the episodes I've ever seen (with rather more tongue-hang than in the comics), and was in the opening sequence, so I imagine he was Superboy's faithful companion across the entire series, à la Tusky over in Aquaman. I'm sure someone will confirm that. Since they're hard to find, here are Wikipedia's synopses for episodes that feature Krypto most prominently:
Season 1 (1966–1967)
"The Spy From Outer Space" – Part 1 - Krypto encounters an alien spy who creates disasters on Earth as part of an invasion attempt.
"The Spy From Outer Space" – Part 2 - Superboy must be rescued by Krypto when he follows the spy to his home planet and the system's red sun drains his powers.
"Krypto's Calamitous Capers" - A criminal scientist has created a sonic beam transmitter with which he can cause Krypto to turn belligerent.
Season 2 (1967–1968)
"Krypto, K-9 Detective" - Dog thieves are on the rampage until Krypto, posing as an innocent dog, is captured.
Season 3 (1968–1969)
"Forget Me Not, Superdog" - Breaking up a meteor shower, Superboy and Krypto are struck by a kryptonite meteor, which gives Krypto amnesia.
Well, happy hunting, I guess.
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