Some of my favs:
God Loves, Man Kills X-Men graphic novel. (basis for the second Xmen film)
Wolverine Mini-Series #1 (part basis for the last Wolverine film). He actually fights the ninjas in the comic.
Xmen - Anything with Claremont was solid.
Alpha Flight (early stuff) && I think the Xmen & Alpha Flight mini-series (it was only 2-3 issues IIRC) w/ Loki would make a pretty solid superhero drama film.
Frank Miller's stuff.
TMNT - I remember seeing issue #1 in a comic convention in Eastland Mall. I was a broke kid but my friend bought it (edit: before it was popular)
I'm sure the Huddle can provide at least another 1000 (minimum) titles/story arcs to read.