I wasn't really going to get into this, mostly because I tend to avoid this sort of thing. Also, I don't maintain any kind of list, so it's all off the top of my head, and I'm certainly overlooking stuff I love. But I couldn't get it out of my head, so keeping all that in mind and the random-ish nature of the rundown...
(Oh, and pardon the semi-arbitrary Age breakdown. It just made it easier for me to keep the stories straight, rather than throwing out a completely arbitrary list.)
Golden Age (1938-1954):
- Amazing-Man's origin, Amazing-Man Comics #5 (1939). It's just that much fun, in a pre-comics Pulp-ish kind of way.
- Daredevil Battles Hitler (1941). To be fair, it's not actually that well-written, but it's still a fun idea. I was recently telling someone that I find it fascinating that Gleason, Feature, Harvey, and other companies floated teams, but the only Golden Age team that stuck was actually designed as a thin excuse to carry an anthology book!
- "That's Madelon!," International Comics #1 (1947). EC did some nice non-horror work, and Madelon was...well, she's a photographer-slash-crime-fighter in France. It sounds stupid, but it's a good superhero story, even if she's not one.
- "The Gun That Dropped Through Time," All-Star Comics #53 (1950). It uses one of the most novel time travel models I've seen, and can only point to one possible precursor from the pulps. Plus, it's a fun story.
- There are also a lot of Green Lantern, Flash, and Dr. Fate stories that I've enjoyed, but none stand out as individuals.
Golden Age, Honorable Mention:
- "The K-Metal from Krypton" (1940). Never published by DC, but the story has been recently reconstructed and is not only good, but shocking in seeing what Superman's creators would have been willing to do with the character's world, had they not been editorially overruled. Comics in general would certainly have been very different, had this hit the stands.
- All-Negro Comics #1 (1947). I obviously haven't read any more of it than has been posted here, but it was a good idea and seems pretty well executed.
Silver Age (1954-1970):
I can think of surprisingly few Silver Age stories that stand out as "the best." I know the early DC stories almost by heart, at this point, and am fond of just about all of them (Atom, Hawkman, Green Lantern, and the Flash, I'm talking about).
Silver Age, Honorable Mention:
- As Narfstar mentions, "Crisis Between Earth-One and Two," but I have to admit that even this is mostly in retrospect, because it's exactly the plot of "Crisis on Infinite Earths," but digestible and written more smoothly.
- Unnamed Blue Beetle stories, Captain Atom #83-86 (1967), and leading into Ted Kord's series. I've got nothing against Charlton's prior Beetle, but these stories are quite good. This is actually "honorable mention" because it doesn't fit stylistically with the Silver Age, in my opinion. It's very much a post-Code-change storyline about a hero who isn't in the good graces of the people, yet.
- "Doom, What Is Thy Shape?," The Brave and the Bold #76 (1968). The Plastic Man that DC should have been using all along. It's here, because the next part of the story doesn't show up for another couple of years.
Bronze Age (1970-1986):
- "C.O.D. Corpse on Delivery," The Brave and the Bold #95 (1971), which I won't spoil for anybody...even though I already have.
- "The Assassination Of Batgirl!," Detective Comics #491 (1980), made Batgirl a hero for anybody who had any doubts. Unfortunately, the writers liked the doubts better. Oh, well.
- Like Powder said, "Crisis on Earth-Prime" (1982) might be my favorite, period, though maybe mostly via nostalgia. Besides being a huge, complicated story, I'm pretty sure the middle chapter was my first non-Batman comic. And I didn't know about anything like a "comic shop," so there were also no such things as back issues. I spent YEARS trying to find the first two chapters of that story, and became a permanent fan of the Golden Agers. Feel free to throw that in the face of anybody who says that the DCU was impossible to follow before Crisis on Infinite Earths "fixed" it. I was nine, and was perfectly happy following the story across four Earths, three decades, five or so teams, and divergent timelines in a story I only read starting halfway through.
- "Night of Passion...Night of Fear!," The Brave and the Bold #197 (1983). Alan Brennert tells us how Earth-2's Batman and Catwoman fell in love. Brennert writes far too few comics, and his entire output could easily make it to my list; as it is, one other will.
- "Generations," Infinity, Inc. #1-10 (1984), which gave some new depth to Earth-2 than a bunch of Golden Agers who are inexplicably not retiring. Unfortunately, the series didn't really hold together afterward, but these are the only books I can ever remember being impatient for the next installment.
Iron Age (1986-2000):
- "Gray Life, Gray Dreams" and "Gray Madness," Justice League #5-6 (1987). This was before Giffen and DeMatteis degenerated down to effectively self-parody, and while there are funny moments, the story hits pretty hard.
- "Should Auld Acquaintance Be Forgot...," Christmas with the Superheroes #2 (1989). The other major Alan Brennert story, where dead and forgotten Supergirl reminds Deadman what being a hero is about.
There were a lot of creative ideas running around these days, but they were never really implemented correctly (Byrne's Krypton) and were saddled with obnoxious heroes (Miller's Batman), so there isn't much I particularly enjoyed about these days.
But as an "honorable mention" series, Steve Englehart had an amazing run on Green Lantern Corps, running through "Crisis on Infinite Earths" crossovers through the series cancellation. There were some nicely creepy possibilities that were never quite brought to the surface, implying that there was something huge in the offing for the Green Lanterns. A shame it never materialized.
Modern Age:
- "The Century War," JLA 80-Page Giant #3 (2000). I should hate this. It's clearly a bunch of fanboy "shout-outs," winks, and nods wrapped up in the sort of story that we were never supposed to see again after Crisis. And yet, it's brisk, clever, and even sweet.
- "Soul War" (2003), JLA/Spectre mini-series. Again, this should've been complete garbage, but it's actually the story that sold me on the possibilities of the (then-)current versions of DC's lineup. It also explained and resolved the reasons for Batman whining every time Hal's name came up in conversation. It's a pity that nobody at DC read this...
And, of course, there's plenty of stuff I haven't read, which I'm sure is fine storytelling (my knowledge of Marvel is minimal at best), and since this was mostly off the top of my head (a dicey proposition with Internet access), it's also poorly edited and probably overlooks stories that I've read and enjoyed, and might even be better than those I've listed here. Sorry on all counts.
I have no apologies, though, for not listing anything by Moore, Miller, Wolfman, Morrison, or any of the other fan favorites over the years. I have literally never read any of their work that I could honestly say that I enjoyed.