My top three Marvel arcs in the past 15-ish years are below. Some have already mentioned them, but I have also explained why.
Grant Morrison's run on New X-Men. At the time it was a welcome shot in the arm the X-books needed. It reinvigorated the line and was a fresh take. It had that excitement all the way down to your gut feeling that is so hard to find. The artwork is grossly uneven, and the ending isn't as good as it could have been, but overall it is my favorite X-run bar none.
Punisher MAX by Garth Ennis - This is a realistic, unfiltered crime story and somewhat of a character study of the Punisher. No super powers, no tights. Lots of scum of the earth getting what's coming. It is grounded and not at all in the regular MU and it was one of, if not the only consistently good book on my pull list every month. Every issue was good. Some were better than others, but it was a great run. Good rotating pool of artists, too.
Would you believe I forgot number three as I was typing? Anyway, here are my honorable mentions. It's possible one of these was the other one.
Joss Whedon's Astonishing X-Men." If you like nostalgia, classic X-Men, and witty dialogue you can't really go wrong. Stunning artwork in the first arc, too. The first arc is by far the best.
Ed Brubaker's Captain America - This was the first time I've been interested in Cap. Great writing like a spy thriller and great art. It gets a little wonky once all of the events interfere, but the core plot and Winter Soldier story are fantastic.
Peter Allen David's X-Factor (2000s) - While this one suffered a bit due to editorial interference (direction changes, cast changes, working around events) PAD just works wonder with these characters, and it's pleasant to read. It's like a soap opera a bit in it's more about following the characters than the plot, but very enjoyable.