If you're talking about specifically-ninja fighting methods as exemplified by Togakure ryu, they're fairly specialized. They were used by intelligence agents and by reconnaissance & guerrilla warfare types; and back then, just as today, a pitched battle was the absolute last thing they would want to be involved in. Accordingly, the fighting methods are particularly suitable for things like resisting/escaping arrest or battlefield capture situations; fighting in darkness or low-light conditions; etc. Hatsumi sensei has stated that someone trained only in the ninja fighting skills would have little chance in a "stand-up fight" against a well-rounded samurai (whose life basically was all about combat). Having trained for twenty years now in both the ninja and samurai martial arts of the Bujinkan, I agree with him.
On the other hand, if you're talking about the martial arts of the Bujinkan in their totality, that's a different kettle of fish entirely.
What does it for me is that the training is principle-based rather than technique-based (even though there are about a gazillion techniques). It is infinitely adaptable and capable of addressing any situation you can imagine, any "fighting range", and is adaptable to any weapon including use of firearms. (Hatsumi sensei has said that any true martial art does not need to fundamentally change just because technology changes: It simply incorporates the new technology into the existing knowledge base in a way that will allow the practitioner to make the most effective use of it.)
I also like the philosophy, which is one of protection of life and living in accordance with nature, or "divine law" if you like.
The only other martial art I have examined and personally experienced which is really comparable to it is Russian Systema.
