I'm going to second Houses of the Holy. The guys original ideas are really good and that takes up the first 7 or 8 chapters, which involve Naruto at a young age training and participating in the Ame civil war alongside Konan and Pain. Arc ends with Pain's win over Hanzou.
Second arc is the regular Chuunin Exam arc and it starts out being bogged down because he rehashes what happens in the manga, not a strong point of his. The last couple chapters have been on the upswing as he moves back to more original ideas. Probably my favorite Naruto fic at the moment.
http://www.fanfiction.net/s/4512691/1/-Medicinal Lullaby Naruto/Sakura
Near the end of Naruto's training trip, Naruto sleeps with a girl and gets her pregnant unintentionally. After the Naruto learns about Pain killing Jaraiya, but before he goes with the toads she shows up on his doorstep 8 months pregnant. She moves in with him and then Ame attacks Konoha and Kisame sneaks in and attacks pregnant girl. Naruto takes her to hospital where the baby is saved but she dies. Naruto goes into hiding and raises her away from Konoha. Story is mostly the years that Naruto spends in hiding training and raising his daughter. But is just now progressing past that. It's a well written story that I enjoy.
http://www.fanfiction.net/s/4087763/1/-Whirlpool Country Naruto/Sakura
Naruto sets up an outpost where Whirlpool Country was and learns about his heritage. Kushina and Rin are alive in this story.
Bullet Tooth Tony: You should never underestimate the predictability of stupidity.
Reporter on Titan Maximum: Sasha is there any connection between your poor album sales and the fact that it sucked?