" My top 3 would be:The Kurama clan is filler. Do we take into account characters/clans not created by the author here on Anime Vice? I don't think so...or ???
Bloodline Trait of the Kurama ClanEvery few generations a member is born who can create genjutsu that are physical objects rather than just illusions in the mind of the victim. You can do pretty much anything and make it happen in the real world. It usually drives the person insane because it's hard to control it to where everything you imagine doesn't seep out into reality, but it's a pretty powerful technique nonetheless.
The Thing Danzo DidI think it's called Izu or Iza-something. It basically allowed him to shape reality as he saw fit, allowing him to negate unavoidable attacks, but at the cost of instant blindness in a sharingan user. I don't think there was any way to actually avoid the technique or defeat it. The only weakness is the aftereffect of going blind, but having multiple sharingan eyes eliminates that issue until you run out of them.
Kabuto's ResurrectionThe strength and worthwhileness of it is totally dependent on who is resurrected, but in the right hands and bringing back the right people it gives one person an insane amount of battle power. There are other techniques that I think could potentially be stronger or more useful, but they rely on personal skill and combinations with other things while these 3 stand on their own and aren't easily defeated or require other things. "