Originally Posted by
Ascended
On top of many of the recommendations here, I'd also like to throw out Exile, Our Worlds At War, the early 90's Bizarro story (I forget the title/issue numbers, and have no idea if it's collected in trade so hopefully one of our more knowledgeable members can enlighten you here) and the Clone Wars story leading up to Action 700.
In Exile, written in the 80's, Superman leaves earth because he fears he might not be able to control himself and could pose a danger to humanity. Its the kind of angsty, soul-searching tripe I typically hate in Superman comics, but its Superman exploring deep space and having some really balling adventures, so despite its post-Crisis misunderstanding of what Superman should be, it's fun as hell.
Our Worlds At War, for me, is the last great Superman epic of the 00's. It ended, ironically, shortly before 9/11 and is essentially a big company-wide throwdown between Darkseid, the American government (lead by President Lex Luthor) and Brainiac. Lots of fun concepts and big crazy ideas. Its not the best Superman story out there. It is, really, rather sub-par compared to many of the stories listed in this thread. But its fun, empty summer blockbuster type entertainment.
The Bizarro story re-introduces us to the post-Crisis Bizarro and is quite tragic and wonderfully handled. There's also a Toyman story from the same era that drastically re-imagines Toyman as an Arkham worthy psychopath, which I find infinitely more interesting than the dorky D-lister he typically is portrayed as. But again, I couldnt recall issue numbers to save my life so either Google or someone else will have to help you with that.
The Clone Wars story (or was it Cadmus Wars? I forget, but there's no Jar Jar Binks so either way, you win) unfolded from shortly after Superman's return from death and culminated in Action 700. Really, most of the early 90's "Triangle era" is worth reading, and Action 700 is what capped off everything that the titles had been building towards since Superman died. This was the era that made me a life-long Superman fan (even though I later came to realize how far off base some of their ideas and treatments were :P )