Oh god, just a few. Let's see what I can write out before I need to run to work...
The Thunderbolts arc with Norman Osborn (starts here
[link]) Which is basically a bad guy group working for the good guys. It has some of the best bad guys (Green Goblin, Bullseye, Venom, etc), so it's really fun. Great storyline.
Punisher: Frankencastle, in which the Punisher gets revived as a Frankenstein monster. XD It's actually really cool, despite the premise sounding... off. This followed a Punisher arc called Dark Reign: Punisher, which was -fantastic-. (
[link] and then
[link])
Incognito, which is just a one-shot with original characters, so not technically marvel. It's about a retired villain trying to adjust to a normal life. They're continuing it, which is good, because I definitely wanted more after this book (
[link]).
The Dark Avengers, which would technically follow Thunderbolts. More goodness with my Green Goblin. Also with Sentry, a very very very schizophrenic 'good guy' that the bad guys manipulate onto their side (
[link])
I could go one. >_> THIS IS WHAT I DO WITH MY SPARE TIME.