1. Naruto- He's really a cool character if you really think about it in a certain way. He doesnt give up, he keeps going. He's like a civil rights activist. Even when bull**** is strong, he just walks forward. Also he's a badass battler. When he fights he always pulls something out of himself that we wouldnt expect and he's only lost one fight, and that was to Sasuke who he was trying to bring back, not kill. Sasuke had originally intended to kill him as well.
2. Kakashi/ Jiraiya- Kakashi dishes out some sweet jutsus and lines. Not only that but he's def a "cool guy" type character.
Jiraiya on the other hand is like the Master Roshi of Naruto. He's a funny pervert. He's pretty strong as well, and his toad jutsus are cool if timed right.
3. Sasuke- Yes, I can smell the haters out there. He's a great good-guy-gone-bad character though. He gets saved a LOT. But you cannot deny that he is strong himself. His eye techniques are shown to be surpassing Itachi, he's defeated Orochimaru (even though his body was rejecting him), Deidara (who, even though he blew himself up, still LOST), and gave Itachi a good battle (didn't really "defeat" him, as he had planned his death and had an illness in the first place).
4. Orochimaru/Madara- Good villians, Orochimaru was essentially "immortal", in his own way. He was impossible to damage completely unless you like obliterate him. He had to get sealed to actually get removed from Naruto, and even then he may make some form of appearance in Kabuto. Not only that, but he could switch bodies, which gave him a longer lifetime.
Madara on the other hand is just so sinister. He can't be hit. You can feel his "evilness", just by the way he talks, and he manipulates well. You also never really know when he will show up (e.x: quit your whining Raikage, you still have a chance, teleporting behind Naruto in the Land of Iron, in front of Sasuke, "its within my powers") He just seems to be everywhere, and he has a lot of insight. He even knew Sasuke would change his name from "Snake" to "Hawk". Not only that, but he MUST be stronger than Itachi. Itachi woulda taken him out to insure he wouldn't touch Sasuke.
5. Pain- He really did his homework. He knows about revenge and peace. He was going about it the "wrong" way, but he was willing to try. Not only that, but Deva Path always looks badass :-D.
These are my top 5 characters that had some real manga time. They arent in a paticular order, and yes some characters are tied to me. The Fourth Hokage should also be up there, couldn't fit him in :-/.