I don't think there's an accurate list of instances that gives multiple and x1. It's all about luck and RNG.

Actually.. :) Higher level instances that give lower tiered materials give more materials than other instances. Like for instance the one i know off the top of my head, "Sparring" for ninja boots gives 2 ninja boots, while all the others give 1.

I can't give you a list, but always aim to do the higher level stuff. :)

Ahh yes, I forgot about materials on instance, I'm kinda thinking about elite instance. There's also 1 remember, maiden's genjutsu gives 2 wind material (I can't recall the name).

"Seal Unlocking Battle" gives 2 Med Kits
"Hidan and Kakuzu" gives 2 Explosive Runes
"Sparring" gives 1 or 2 Ninja Boots