And the only reason I didn't include Justice League #1 is that it was already mentioned in the initial post.

Other than ASS #1 and Superman #75 I can pretty much rule all of the others out (in my mind) because I don't actually know what they look like.

In the current decade though, it's much harder to pick standouts, as too many titles are saddled with Marvel's non-descript "iconic"(really, generic) covers or Alex fucking Ross.

Anyway, my picks for the current decade:

ASS #1 is only not the greatest comics cover ever because its value comes as a response to Action #1 and the next 75-odd years worth of Superman covers. If it's you're first glimpse of Superman, you won't get it, but it is perfect and beautiful in every other way.

New X-Men #114 is homaged (badly) in New Avengers #1, I can't believe no one else has mentioned that. Yes it goes for action movie cool, but it pulls it off.

American Virigin #1 no more Quitely, I promise, but this one is real standout on a medicore title.

Infinite Crisis #6A I generally loathe Jim Lee, but the imagine of Superboy in the Anti-Monitor was a WTF? like no other when it was released and made unable to wait to find out what was going on.

Batman #608 Lee again, though reluctantly. The first issue of his Batman run is well-remembered and changed how artists have to draw boots.

Planetary's Rubber Soul cover (#8?) All of Planetary's covers are homages of a sort, but this one transcended that and no other cover as much says Planetary to me as this one, as the odd, distroted angle is just perfect for the series.

Final Crisis #2A the oppresive Chip Kidd cover design works perfectly well with the shocking image of a crucified Batman.

Superman #75
All-Star Superman #1
Batman #497 (whichever one where Bane broke his back)
Green Lantern #49
Justice League #1 (might not make the date cut, I'm not sure and I'm too lazy to look it up)
Captain America #25
Kingdom Come #4

I can't think of the issue # but there was an Amazing Spider-man cover from JMS' run that was burned into my head.

Would also add Wolverine #1, Kingdom Come #2 and New Mutants #87. Is going back 20 years too far?

The cover to the original JLA/Avengers....obvious cuz it's George #$#$#$ Perez. Weird, cuz the book was never published.

http://vu.morrissey-solo.com/moz/perez/cv/ci6.jpg

(I can't find a copy of the actual cover)

A bit too early for this. And yeah, I thought he was taking a crap as well.

You should start a second list of covers that you think should be widely remembered, but aren’t. I’d start my list with Alex Toth’s Batman Black and White #4.

TBH, that seems to be what most of the answers people are giving are.

I can't answer so much for the Marvel ones (really the only Marvel cover that is iconic to me personally is that one with Peter Parker dumping his costume in a bin and walking away), but the only two I can honestly agree with are Superman #75 and All Star Superman #1.

That Alex Toth cover is fantastic though!

It certainly popped out of the 711 magazine rack to my 11 year old eyes.

http://www.comics.org/coverview.lasso?id=40893&zoom=4

And I agree with Andrew above who said that New X-Men #114 doens't strike me as iconic because, as nice an image as it is, if you swapped in other characters for the X-Men, only hardcore Morrison or X-Men fans would realize it was an homage and not just an attempt to simulate the "characters walking toward the camera in slow motion" shot you see in so many action movies.

As for the most recent one ... I can agree with All Star Superman #1 (I don't actually like that cover - it looks too much like Superman's going to the bathroom in a cloud to me - but I can easily see it being homaged years from now).

Also, Runaways #26.

Also, on the subject of covers that homage other covers or works of art and whether later covers can be homages, I think that the nature of the homage is in what the artist intends to homage when he draws the cover image. If an artist was thinking of the issue of X-Men with Cyclops holding Xavier then that's the cover being homaged. If he was thinking of CoIE #7 then that is the homage. There is no transitive property of homage that makes any use of that pose an homage to the Pieta.

http://apps.facebook.com/comicbooks/editions/runaways-v2-2005-18-parental-guidance-conclusion/cover

I don’t think I’ve even read it but it’s always stuck in my head."

Honestly, my favorite cover of all time, but I don't think that it's iconic. It's never been homaged, it's never been worked into an interior, and to the best of my knowledge, it's never been used on merch. I just don't think that unfortunately, the Runaways are big enough to produce something on the level of a Year One Batman cover.