hmmm.....there's a lot here so I'll put up some recent stuff that I've loved:
Spider-Man Reign. Alternate future spider-man comes back after MJ's death. Now this isn't for everyone, but I ****ing loved it. One of the saddest, most brutal Spider-tales ever that really hit on the character's responsibilities, selflessness and that effect on others. People often ask what's the difference between this and the dark knight returns. Batman's always batman in batman, he wins even when he losses. The outcome of that was always definate. In this peter comes back and he knows he'll die. The man sacrifices himself to save others and in doing so he's rewarded in kind. This isn't about a hero just saving the day, it's the effect that hero has on others. Plus the art is great, best version of venom (and character understanding) ever ever ever. And there's one part of this book that if you don't cry, you're just a monster.
Spider-Man/Doc Ock Year One: Want to know why doc ock is one of the all time best villians? Read this. Great art, amazing characterizations, ock is at the same time terrifing, sad, sympathetic and insane. The end also sets up their rivalry better than anything I've read to date.
The Evil that Men Do: a very delayed but pretty good limited series done by Kevin Smith. It's a pretty good portrayal of felicia hardy but the main draw is the guests stars and spider-man talking. They have a real friendship that's often missed in spider-man tales.
I'm with Stupid: Not sure if this is trade yet but it should be. Very funny oddball tale about the friendship between pete and the human torch. The art is old school the tales are old school but surprisingly funny and touching. This is slott at some of his best.