Heroes:

String Theory--A massive epic involving an alternate Peter and Hiro attempting to change the world by going from dimension to dimension. There are twenty-six universes in all, and each is different from the rest. A truly creative fic, one I would recommend if you have the time.
http://www.fanfiction.net/s/3555388/1/StringTheory

Alternate Universe--yet another "what-if-Mohinder-met-Sylar-before-he-started-killing-people" fic, except it is extraordinarily well done. No, seriously. It's a genuinely well-written love story, and much better than some of the romances I've seen published.
http://violet-anchovy.livejournal.com/1568.html#cutid1

Naruto:

Creating a Family--This is a crack fic done right. Pretty much, Itachi Uchiha decides to rebuild his family, and does so in the most disturbingly hilarious manner possible.
<a href="http://www.fanfiction.net/s/2928732/1/CreatingAFamily">http://www.fanfiction.net/s/2928732/1/CreatingA_Family

There's more, but it's 2 in the morning and I'm dead tired. I'll post the rest tomorrow.

I'm gonna rec Ciceqi's Mascotverse (FFVII, currently mostly pre-game, pretty much AU- not Crisis Core compliant, for one-, Sephiroth/Zack/Cloud/Aeris in different combinations), Chibirisu-chan's Wark With Me, Kid (FFVII, pre-game, quite possibly not Crisis Core compliant, vaguely Sephiroth/Zack/Cloud), and The Shape of His Heart by Gabi-hime (FFX, during the game, Auron/Rikku, more or less).

I'd also suggest having a look round No True Pair and maybe Fictunes, see if there's anything you like.

I've been thinking, maybe we should start an archive for goodfic. I'm guessing most people here enjoy fanfiction--that's why we go through so much effort to spork badfic. But it would be nice to have a place of refuge where we can relax and look at some goodfic.

I definitely have contributions to make to this list, but I've got homework right now, so I'll drop by later today to put up some links.