Greetings all, hope you don't mind if I join the party. Anyways, two really good fanfics I've read on fanfiction.net were a naruto one, Chunin Exam Day, and a Megaman one, RockmanEXE: The College Years. Both stories are long, well written, and have a number of laughs with them.
Chunin Exam Day is a timeloop fic where Naruto get's stuck and has to repeat the chunin exam agin and again until he makes chunin, and possibly save Konoha as well. The College years one is just as it sounds, everyone goes to college, but still ends up fighting evil net terrorist organizations, only finding love along the way as well. Quite possibly the longest story on the site.
Also, arfran5890, do you have a link to that Yu Yu story?