I guess I'll just pull out some Naruto stories from my favorites list that haven't been mentioned yet:
The Lazy Uchiha by Hibiki54
A self-insertion story of story of sorts (*gasp*) that's presented in the oddest way possible. Itachi in this fiction is a completely different person - a lazy bum, but a genius nonetheless - and changes things around for better or for worse.
This Time Around by Crimson Skies
One of those 'Naruto gets sent back in time to fix everything' stories, except Sasuke is dragged along for the ride. Presented in a way that's more than tolerable, but actually good.
About a Daddy and a Nanny by syaoran no hime
A Neji/Tenten fic that I couldn't put down. The humor the author puts in this story is just pure gold.
Hana Ni Arashi by Raina1
An OC-centric story, in which the main character is Sasuke's daugher. The character might be slightly on the Mary-Sue side, but the side-stories and the way other characters interact with each other more than make up for it.
The Reinvention of Memory by Luc Court
This one-shot features the most believable (in my opinion) and realisitc way Sasuke redeems himself, returns to the Hidden Leaf, and reunites himself with Team 7 as well as getting along with the new addition: Sai.
Through the Glass by Novice Named Jack
Naruto falls into a coma, only to wake up years later and finds everything changed - for the worse. A story that puts Naruto through harsh times, but a glimmer of hope can be seen at the end of the road.
Naruto: Unleashed by FireTemptress
This story is hard to describe so I'll just give what the authoress wrote for its summary: "Orochimaru and Itachi still live. Yondaime's seal is weakening. There comes a point in everyone's life when they finally snap and the demon in them takes over, but when it concerns Naruto, it's exactly what everyone fears." A NaruSakuSasu threesome pairing.
Speaking of threesome pairings:
Teamwork by Asuka Kureru
Probably the best threesome pairing fanfiction out there. Be warned, mature themes!
Catch 22 by The Sh33p
A series of five 22 little glimpses into a possible Naruto world. There are a few ideas I actually borrowed from this piece of work (with the author's permission of course) and they have been incorporated into my story, Medusa Javelin.
Point of Origin by Garret pi
A Naruto story that looks deeply into politics. A well-structured story that adds more realism into the world of ninjas.
Between Sun and Moon by Kaara
The only Naruto/Ino story I was actually facinated by and was the only story I could tolerate (besides the story
Team 8 by S'TarKan) in which the story replaces Sakura with someone else for Team 7.
A Final Hit by NoiseTank13
Perhaps the MOST depressing story I have ever read, and that's saying a lot, coming from a guy who had been critized by many to have made them depressed and cry by writing Garden of Sanctuary. Nevertheless, the plot in this story is brilliant, and it is such a shame that the author had seeingly abandoned this could-have-been-great story.
And now, for some Naruto crossovers. A genre which I, oddly, rather like:
Bleach Crossover:
How to be a Mr Nice Guy by James Ray Edward
Humourous, and a unique writing style makes this one of the most addictive stories out there (in my opinion, of course).
Ranma 1/2 Crossover:
Invictus by YamiPaladinofChaos
One of those dimensioal travel pieces that doesn't seem to mix at all, but again the author manages to pull it all off somehow so the interations between the chracters seems all so real. Also, the author of this story does something most other authors do not when people slip through dimensions - they also explore what had happened to the people left behind.
Samura Deeper Kyo Crossover:
Tenkage by moguera
Two words: ninja clash!
Berserk Crossover:
Naruto: Berserk by Lousy Poet Automaton
Good god, this is a brilliant piece of work. Not only does the author pull off something unique like crossing over two genres that seem totally unrelated with each other, but does an awsome job at it. If you have ever read or seen Berserk (manga and/or anime), then read this. It won't dissapoint you. And even if you haven't, it's still a very enjoyable read. Be warned thorugh, some dark themes.
Harry Potter Crossover:
Masks and Shadows by Kilerkki
This fanfiction stands above all other Harry Potter/Naruto crossover fanfictions for one reason and one reason only: Naruto characters in this story cannot speak English! (Well, not good English, anyway) Whenever I read Harry Potter/Naruto crossover this ALWAYS bugged me, and I was so happy when I found this story and how the author actually didn't shy away from the language barrier problem but actually uses it to its advantage! A very well done piece of work.
That's about it from me! Hope you enjoy!