I know of several good ones.
Caged Fox has several good ones, and he isn't afraid to kill them off.
Lacking Sight has some that play pretty big roles, but are done nicely. They are fallible and that really helps.
Sic Semper Morituri has a few main ones and some minor ones. That is one really long fic, and I don't think it is really anywhere near completion.
The thing with OC's is that usually, the characters end up altered anyway to be non-canon, and thus become original yet still based on existing characters. Also cases where a character has so little canon characterization that there is no choice but to make up stuff. Kyuubi ends up one such character quite often. Rin and Obito are kinda like that. Obito has more information about him, but not all that much is known about Rin. Many times the main characters are altered yet still fit decently well. Ranma in Just Won't Die and Path of Chaos are in ways similar, and yet different. Naruto can range from being a complete moron to a genius to a broody bastard or anything basically, just hiding behind a mask. When a person writes a character, they make their own version. These differences come up even with official versions. Differences from manga and anime, or in the case of Tenchi, multiple versions.
If a person can create OC's then they are basically ready to create everything on their own. They understand how to use archetypes and can probably make use of the
36 Plots. Someone made two more unofficial ones but I forgot what they were.