Favorite Comic Book Story line or issue.

[God Magnus]

A semi-recent mini series that I love is Batman Year 100. It won me over the way The Dark Knight Returns did when it first came out. Paul Pope does wonderful things with the character, boiling him down to a very gritty essence. It also celebrates the history of Batman in an interesting way. Even now as I reread it I keep thinking "If the regular Bat-titles were as good as this right now, I'd still be reading them."

 

[Snaploud]

The Life and Times of Scrooge McDuck by Don Rosa.

 

[Derishton]

Simonsons' Ragnarok run on Thor.

The Flash issue with the plane mentioned above - maybe the single greatest single issue of the last few decades.

Spider-man, Kraven's Last Hunt.

Most of the Giffen/DeMatteis JLA era (not the European one as much).

Fables is amazing up to vol. 7, which I'm about to read (I assume it remains amazing).

Sandman, Season of Mists.

The Walking Dead.

 

[Mr. Laser Beam]

Strangely enough, I kind of liked Camelot 3000.

And DC One Million.

 

[C.E. Evans]

I think my favorite of all time was Onslaught. He came in quietly, pretty much kicked everybody's ass in the Marvel Universe, and then discovered that he was merely a psychic projection borne from Professor Xavier's previously repressed dark side. Nearly destroyed the entire Marvel Universe, but from Onslaught we got Heroes Reborn and eventually Heroes Return.

I also liked when Despero appeared in Justice League America in 1990. During most of the Giffen-DeMatties-Hughes run, JLA was a book more known for its sense of humor, but no one was joking when Despero returned and caused death and destruction everywhere he went. Despero's merciless carnage was a none-too-gentle slap in the face in an otherwise fairly light-hearted book at the time...

Honorable mention:
CrossGen's Negation. Every frakkin' issue. 'Nuff said.