I'll be talking in the aspect of a treasure as a whole including Rares and Super Rares. (Not commons)

First we have to define good in a PvP setting and a PvE one.

In terms of Kage PvE

Gaara Kazekage
Darui
Mei
Onoki
Danzo

These ninjas are great for 9tails over all letting you auto 9tails the whole time. Also Gaara Kazekage (and non) can be used for Ninja Exam for majority of 120 - 180. I'll assume the same goes for the other rares as well. These ninjas are also great for TI that can boost you and your teammates.

In terms of Kage PvP

Killer Bee
Mei
Mifune
Sasuke
4th Raikage

Killer Bee buffs every Jinchuriki, common ones you see are Kurama Naruto, Roshi, Kushina [Mad Momma]. To increase their damage and make them a bit tankier. He c*so let them attack 2x for 2 rounds and make their mystery unable to be interrupted.

Mei is a bit harder to run in PvP, she can easily boost the damage of P1 Shark Bombs with barrier. However it requires a lot of initiative to win the barrier fight and you need to hope there is no Shark Kisame/Roshi/Madara 5 Kage. It c*so let you do the generic GNW tenten/Mabui set up which can still be good depending where you're at in the game or where your server is at (GNW Speaking)

Mifune unfortunately, sees a lot less play if none at all, but he can remove buffs and shields on his target while buffing Sword Ninjas. Sadly, there are better ninjas that do it better.

Sasuke the most he can do is deal a lot of damage on mystery, outside of that he is immune to pure ninjutsu, so if Sharkbomb hits him for example, he won't take damage but he can still be Chaos. To really get him to work you'll want Shisui and Itachi Anbu if you really want him as your main damage dealer. Outside of that, he falls flat in a lot of areas.

4th Raikage unfortunately, this ninja requires Samui which is in LoL to actually be effective as she can essentially choose a target and have 4th Raikage blitz them down. This ninja is more of a arena ninja imo just cause how easy it can be for him to kill mains turn 1. Of course, he also needs a lot of buffs to really start wrecking people and as many as possible, so you'll want any ninja that boosts Lightning ninjas on barrier such as Sasuke, Darui, Danzo, Shisui. However, because Samui is mandatory, you'll NEED Darui since he can attack 2x under the barrier and give more chakra. Unfortunately, ninjas like MM can shut 4th Raikage down (Darn those Uchiha!) While he does offer a powerful turn 1, he does fall flat turn 3 if ninjas are still around and able to fight back. It also doesn't help when a lot of ninjas either dodge or are immune or both.

GNW PvE

Edo Zabuza
Kushimaru
Jinpachi
Jinin

Edo Zabuza inflicts blindness which doesn't matter too much in PvE, however he does gain extra standard attacks, and his chase that is on combos is really nice giving technique points. More of a ninja for Ninja Exam or TI

Kushimaru this ninja is really great for Ninja Exam or TI and able to immobile 2 ninjas can be really powerful in those areas. Some Ninja Exams have easy fodder for him to keep gaining standard attacks (Ninja Exam 207 if I recall). Of course this ninja needs to be buffed by a lot to really abuse him as much as possible.

Jinpachi able to inflict ignition, and give double standard attack and remove 1 layer of debuff to 2 Edo Ninjas is really good. Mostly support and mandatory for nearly any team involving any Edo Ninja.

Jinin mostly a power based ninja, but he can easily rack up technique points if you build around him. He can deal a lot of single target damage.

Madara this ninja CAN replace Asuma in 9tails and probably do really great in all PvE, However, if you run him in 9tails you can only run Konoha Ninjas so you won't be able to auto that much unless you want to use Danzo but there are better ninjas in that case.

GNW PvP

Unfortunately the only real PvP ninjas you need are Kushimaru, Jinpachi and Edo Sasori so I'll * to those 3. Sorry Ameyuri Ringo and Zetsu, you both don't do anything.

Kushimaru I already stated what he can do, so it should be obvious why he is good in PvP, especially when Wind Main is a Clone Generator.

Jinpachi, already stated what he can do, so he is thrown into a lot of Edo Teams in general such as Edo Deidara teams and Kushi teams and rarely Jinin teams.

Edo Sasori, buffs all Edo ninjas and gives them a shield, able to resurrect and deal chaos as standard when he is resurrected while able to re apply the buffs, no wonder he is really good for Edo Teams.

Unfortunately Edo Teams fall flat to Madara 5 Kage and friends.

Madara, huge counter to Tai Damage ninjas since he is immune to pure Tai, able to not care about Minato Jonin, Guy Gate of Shock or even Kushimaru. Huge Chakra Generator (kinda) and able to gain up to 3 standard attacks (Anbu Itachi plus standard from Madara's mystery) he can potentially hit really hard if you choose to buff him. Unfortunately, I believe Shisui and Anbu Itachi and mandatory when running him. Still makes him really good over all.

Naruto, I don't know how to start with this one, able to be run with a lot more teams than Madara in general such as Shark Kisame, Jonin Minato, Kushina, Seven Swords Bee, Roshi, way too much to really count. Able to dodge, grant immunity to allied forces for 4 rounds which is insane when combined with Tsunade 5th Hokage, he c*so immobile a ninja through his chase, ignite on standard and if he combos, then reduces his mystery's CD by 1. Unfortunately, the only thing holding him back is the fact he doesn't scale, if he could, he'd be a lot better than he is now. Still a great ninja over all.