You guys are kinda of missing the question. It says who is the best shinobi not the best character or the strongest but who is the best at doing what they are told to do and getting the job done quietly.
In that regard I think the best over all shinobi would be Tobi. Think about it until the near end of Shippuden it seems Tobi has worked behind the scenes manipulating the courses of the characters we watched lives, all in a hopes to achieve his end goal and STILL no one knows who he is, by definition Tobi is the best overall shinobi.
Now as far as who has the most jutsu's determining the best shinobi that without question would be Orochimaru. It's been stated that he dedicated his life to learning as many jutsu's as he could and with all the experimentation he was doing I'm sure he was able to acquire some clan only jutsus as well.
So my vote goes for Orochimaru from this list.