Let's start by saying: I am very bad at making puzzles. So just rule that out okay?
But either way, I'd like some ideas for, well, where to put rare items. I'm talking about items that are really rare. I can't think of a way to have sidequests that yield these items, because nobody would have them, and those who would have them definitely wouldn't want to give it to you. My "best" idea so far is to have it be from another dimension, so... challenge portals? (Portals that lead to levels with ridiculously kinda over-leveled enemies with the item at the end)
EDIT: Oops, accidentally posted without tags, and it doesn't look like I can add tags, sorry. :/