I don't know what my favorite single issue is, but these 3 stand out a lot. I might be forgetting a lot of issues I'd put ahead of these - but, right now...
Fantastic Four #5:

Maybe Doom NEEDED to be accidentally green on the cover - because like the myth about the quilt makers who purposely added flaws to their quilts to avoid the sin of pride - this comic would be too perfect.
Dr. Doom's intro involves a convoluted plot to send the FF back in time to steal Black Beard's treasure. Among all sorts of great things it's got The Thing dressed up as a pirate.

Superman #149:

I think everyone has a slightly sinister desire to see the Coyote get Road Runner just once.
When silver age DC gets dark it gets pretty dark! In this issue Luthor cures cancer in order to gain Superman's trust so he can later kill him - which he does, and there's a whole funeral and everything. (I can't confirm, but I think this the first "Imaginary Story" - is it?)
Cerebus #36

Okay, the cover isn't so hot - but here's the thing --- you're reading this funny book about a barbarian aardvark and suddenly this issue comes out of nowhere and it's got a punchline with actual emotions and you start to realize how fully formed the characters are starting to get. It really shouldn't work as well as it does - there is NO set up to this issue, Jaka comes out of nowhere and there's no indication that Cerebus even cared about her before - but in a way that works out well for the story, because this is an introduction to another aspect of Cerebus, an internal one.
Fantastic Four #5:

Maybe Doom NEEDED to be accidentally green on the cover - because like the myth about the quilt makers who purposely added flaws to their quilts to avoid the sin of pride - this comic would be too perfect.
Dr. Doom's intro involves a convoluted plot to send the FF back in time to steal Black Beard's treasure. Among all sorts of great things it's got The Thing dressed up as a pirate.

Superman #149:

I think everyone has a slightly sinister desire to see the Coyote get Road Runner just once.
When silver age DC gets dark it gets pretty dark! In this issue Luthor cures cancer in order to gain Superman's trust so he can later kill him - which he does, and there's a whole funeral and everything. (I can't confirm, but I think this the first "Imaginary Story" - is it?)
Cerebus #36

Okay, the cover isn't so hot - but here's the thing --- you're reading this funny book about a barbarian aardvark and suddenly this issue comes out of nowhere and it's got a punchline with actual emotions and you start to realize how fully formed the characters are starting to get. It really shouldn't work as well as it does - there is NO set up to this issue, Jaka comes out of nowhere and there's no indication that Cerebus even cared about her before - but in a way that works out well for the story, because this is an introduction to another aspect of Cerebus, an internal one.
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