Alan Moore’s “The Last Superman Story” part 1
Swamp Thing #21 “The Anatomy Lesson”
MiracleMan #15 - the final battle between MiracleMan and Kid MiracleMan
Fantastic Four #50
Spider-Man #33
Fenris
Amazing Fantasy #15.
Setting aside graphic novels:
“Coyote Gospel” issue of Animal Man (#5). Grant Morrison before he lost his balance. Beautiful.
Miracle Man #15 (As good as a climactic slugfest can get.)
Captain Marvel #33 (Starlin at his over-the-top best)
X-Me 153 (“Kitty’s Fairy tale”. Come on, the Dark Phoenix climax is too easy. Besides, I’ve always wanted a Bamf doll.)
Damn near any issue of Sandman, but I’ll single out “24 hours” as the best horror comic ever written. (Close runners up: “the Sound of Her Wings”, “Ramadan”, “Three Septembers and a January”, “Song of Orpheus”, and the concluding chapter of “A Game of You”)
Thor #362 (‘He stood alone at Gjallerbru’) Close second #336.
Swamp Thing #50 (Best damned “ultimate battle” ever.)
Daredevil #181 (Miller at his peak.)
“Death Watch” (Avengers Annual 7/Marvel 2 in 1 Annual 2) The last time Thanos was done properly.
I don’t remember the issue # and I don’t feel like digging through my Legion of Super-Heroes 40 year collection, but the best story was when Saturn Girl, Brainiac 5, Duo Damsel and Rond Vidar confronted the Time Traveler. Particularly the panel when Rond says “I said NO” and the Green Latern energy came out.
That was my favorite moment.
Annie: LoSH, Vol II, #46(?)-50. Great stuff!
Um… NightMask #12?
Or, better yet, the older Superman comic (from the 60s, I think) that has Superman trying to puzzle out the whole “L.L.” conundrum in his life.
Or, no, wait! The equally old (once again, I think) Superman comic where Jimmy Olsen is gassed by a rich guy and tricked into thinking that he has somehow time-traveled into the 18th century past. Eventually he finds his way home and Superman exacts justice (maybe the rich guy had a nefarious scheme going on?) by actually taking the rich guy back in time to some Indian war where no one was actually hurt. (Dude, where’s that Bozo2000 guy when you need him?)
But no, now that I think on it, it must be the PowerPack issue that has those super-duper kids dealing with (and claiming victory over) drugs. G’bless the 80s and early 90s. 
(But then, there’s the creepy Teen Titans issue where the gang is dealing with a supernatural changeling demon baby on a lonely farmstead somewhere. I think the Pa–or the grandpa–eventually realizes the baby is a changeling and kills it, thereby stopping the demons and saving the story arc from continuing to a two-parter.)
Apparently the name I meant to say was “BZ00000”; and in this thread. Oops.
I tried to think of a LSH single issue to include. The thing is, while I love th eLegion with a purity that defies all rational explantion, it is the characters themselves who draw me in. When I consider each individual issue as a separate entity, I just cannot find one that stacks up well against the finest work in the field.
Used to love that book, though. (I consider all issues that reflect the moral downfall of Jan Arrah to be heretical and imaginary and absolutely not true and stooopid to boot. So there!)
It’s tough to pick my choice for the best issue of “Watchmen,” but I guess #12 where everything gets wrapped up. Or the Rorschach origin issue.
If graphic novels can count, “God Loves, Man Kills” was excellent as well, as were “The Killing Joke” and “The Dark Knight Returns.”
Those are the ones I can think of off the top of my head, since I haven’t read comics for way too long. Time to dig out the old collection and get nostalgic, I guess…
Lesse, I got a couple…
I have the TPB but don’t know the ish… It was in the second half of the Transformers series. Ratchet, who has been developed as a very haunted character at this point, sacrafices himself to destroy Megatron. I think I was, like, 10 when I first read it. That is what got me into comics.
Batman: Killing Joke. It was a stirring example of the risks Bats and Crew took, as well as how dangerous the Joker was as a villan.
Sandman: Death of Morpheus. It was the first issue of Sandman I bought, and I’ve sought Trade Paperbacks since. It has so much more meaning now.
Protectors #5: Death of Nightmask. Not an especially notable series, but this was an good tale about a rookie superhero who tried to prove himself.
Stormwatch #25: Issued fifteen months early and fitting into continuity, this issue brought attention to an underrated superteam book by teasing a foundation-shaking event for over a year, forcing you to put the pieces together month by month.
X-O Manowar #0: Not much too it, but it reminded me that some comics will always be cool.
Agreed. And on the rest of the list, too.
I’d also like to second/third/whatever, Hob’s first appearance (Men of Good Fortune? Something along those lines), and suggest Dream of 1000 Cats and The Collectors as high on the list, as well.
A few personal favorites:
I can’t remember the number or the title, but the issue of Sandman that showed us what cats dream about.
The issue of Daredevil where The Beyonder gave Matt his sight back for one day.
'Mazing Man #12.
You’re probably thinking of Transformers #59 – Megatron has rigged a set of explosives that will blow up and destroy the Ark. While other Autobots are escaping from Megatron’s base, Ratchet goes to the transporter controls and recalibrates them to bring the almost-ready-to-blow explosives to Decepticon HQ instead. Megatron tries to flee the explosion through the teleportation portal, but Ratchet tackles him and they both go up in flames.
Ratchet has a tendency to do the “noble sacrifice” schtick fairly often. In Transformers #8, he makes a desperate charge at Megatron to try and knock him off a cliff (he succeeded, but not as he had intended). And in Transformers #78, he causes the Ark to self-destruct, killing himself and Megatron and Galvatron to prevent them from running free once more to wreak more havoc.
Hey… where’d everybody go? 
A couple of people have mentioned The Killing Joke. Doesn’t the ending through you out? I can’t work out if it ruins the story or makes it because in the theme of insanity it is about as crazy as you can get. (There is a school of thought which says it was Moore’s way of acknowledging that despite the fact that the Joker pushed the envelope and really would have been killed in a “realistic” story the limitations of the franchise prevented him. Thus, we get this odd ending)
Iron Man #222, because he didn’t have to deal with supervillains in that one, but instead with natural disasters all the while running late for his own party as Anthony Stark.
When the little girl’s cat was on the tree and he snaps and flies off, but returns to fetch the cat for the girl, that was very touching.
Overall, a great issue
Watchmen #11. “I did it 35 minutes ago.”
Spiderman vs Wolverine. Much better than the title would indicate.
The issue of Sandman where Morpheus goes to Hell and finds that Lucifer has quit.
Eh, I always thought that was way overrated.
[spoiler]Spider-Man by himself gave a spankin’ to the X-Men, including Wolverine, in Secret Wars #3, and later took out Firelord, a guy who could give Superman a hard time (but still lose without a doubt) and all of a sudden he can’t take out the Feral Canuck? Spidey would have drowned him in web fluid; Wolvie’s claws are nice and all but if his forearms and biceps are glued to his sides they ain’t gonna be much use.
Then the whole deal with Spider-Man going “Oh my god! I’m in some spy war, this is serious and over my pretty little head!” Whatever. Spider-Man’s had to deal with super-villains trying to kill him for years, and more than a few have targeted his friends and family. What’s the KGB gonna do?
And of course the ridiculous killing of Ned Leeds to make things seem oh so serious. The writer wanted to show the reader that Spider-Man was in over his head, but that just seemed gratuitous to me.
I’m of the opinion that writers have underrated Spidey’s abilities and way overrated Wolverine’s abilities for years and this book was the prime example of that.
Spider-Man may not be an out-and-out badass, but his mixture of abilities should enable him to hold his own against almost anyone you can think of. Limited super-strength (for a comic book hero), super-agility, super-endurance, sticks to walls, has some sticky fluid that Dupont would give their right arm for and has a sixth sense (when the writer remembers it) that warns him of danger and allows him to avoid it it. That combo would make him a tough opponent for 95% of the comic book super-heroes out there.
Wolverine with his incredible healing, super-senses, indestructible skeleton and claws would be a tough opponent to permanently take out, but not to knock down. C’mon, except for his claws he’s all defense. He has zero range attacks and if you box him in a corner he’s out of the game. I honestly like Wolverine, but the writers need to get a grip, he ain’t all that.
[/spoiler]
Regarding the OP, I can’t think of my favorite single issue, but I’d toss G.I.Joe #21 out as being one of my favorites, because it showed me that comics can tell a complete and even somewhat complex story without any dialogue.
“Who is Scorpio?” from Agent of SHIELD in the late '60s–but any Jim Steranko will do; the guy was out there!
–Alan Q
Hellblazer: the second issue of the “Dangerous Habits” storyline (and the second issue Garth Ennis wrote). Constantine meets and old friend in Ireland to help get a cure for his lung cancer, but finds out that the friend is also dying of liver disease. And the friend has made an interesting deal with the devil… Best comic story ever.
About The Sandman “24 Hours,” that’s actually the story that made me stop reading the book. I’d picked up the first issue at random because the cover was neat, and had every other issue up to that one. I hated it so much I stopped buying the comic – then got back into the series much later and found myself having to pay HUGE bucks to get all the back issues I’d missed.
Ambush Bug Nothing Special Special #1