I'm looking for a game systems and/or campaign setting that focuses almost extensively on subterfuge classes/ninjas.
I don't have any setting restrictions - this could be in any time period, or flavor.
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How important is the Japanese/ninja specific part to you, and how important is "all subterfuge" in terms of class options? And do you want modern day or 1800s or "made up fantasy" as your setting?
Depending on whether you demand the Oriental flavor and whether you're looking for a modern setting or not, there are a number of espionage RPGs that are all about the subterfuge classes. Top Secret from back in the day and to a lesser extent its successor Top Secret: S.I., the James Bond 007 RPG, and more recently Spycraft and its second edition. None of these are really specific to "ninjas" though many people made ninja characters simply by skinning (no pun intended) their spy characters.
If when you say "ninjas" you mean more the Warrior's Way/Ninja Assassin type of ninjas, then Feng Shui or Hong Kong Action Theater! are better bets. They don't "focus on subterfuge" but then again neither do those depictions (besides "we hide before leaping out to the killfest").
I can probably be more helpful with more clarification, there's other stuff that may qualify but if this is just a "I thought it would be cool for people to take their time to make a big ol' semirandom list" request I have other stuff to do...
Right away I think of Palladium's Ninjas & Superspies, which I'll admit I've never played -- but which, I understand, does exactly what it says on the tin.
The old Thieves' Guild RPG dealt almost exclusively with living a life of subterfuge. Later supplements to it detailed fighters and magic-users, but as back-of-the-bus secondary characters to the main characters of the game: thieves. In this nearly exclusive focus on one type of character with other characters shoved in the background Thieves' Guild kinda/sorta heralded the approach Ars Magica later took for magic using characters.
Hero Games has a Ninja Hero module that may be what you are looking for. I've used the Hero system for a long time, starting with their most popular Champions superhero genre. I've used it for many different settings including fantasy, sci-fi, horror, and more. I'm a HUGE fan of the flexibility and freedom that it allows.
Spycraft is, as the name implies, all about the spy game. Though in its "modern-world superspy action movie" context it may mean more action-focused than you might want, it has its share of subterfuge classes, even with a straight-from-the-book-if-not-in-name Ninja class called Intruder. The Counter-Terrorist and Raptor Expert Classes also seems to fit the "Action-Ninja" role.
I tend to find that my countryside campaigns focus more on martial skills, and my urban campaigns tend to focus more on subterfuge. In a crowded bar, having the dwarf start a barfight over the Artifact of Foo can be fatal, whereas if the small and lightweight Artifact can be quietly lifted from the Hooded Stranger, the party get the swag with less risk and less exertion.
I might regret this but there is Naruto D20, a D20 Modern based adaptation of the Naruto anime.
This means that you have base classes defined by your strongest attribute, you have your Strength based ninja who could be a great swordsman, a Dexterity based ninja i.e. your stereotypical ninja and Intelligence based ninja's which concentrate on the magic powers japanese folklore attributed to some ninjas.
There are also a lot of prestige classes which have most of the favour in contrast to the generic base classes, their fluff is very tied to the Naruto universe but since every tipe of ninja from demonic shadow mages to plain sneaky guys exist in the manga this is not that much of a problem.
The RPG does a great job of capturing the manga's flavour basically the premise is everyone's a ninja, whether you're more of a mage type or a fighter or your classic sneak-sneak everybody should have basic stealth training and secrets and discovering them is the key to any battle.
If you're a fan of the manga you should definitely check this out, one problem is that the anime is DnD 3.5 in animated form a lot of flavour a lot of options but there are just some powers, those of the main character big surprise, which are just overpowered and it shows.