Hands down, hardest hack in history - Zelda Parallel Worlds. That game is pure hell and amazing for it. Heck, you don't even get the sword and shield NOR the ability to save until very late in the first dungeon! (The dungeon itself is already very challenging) Hidden mechanics such as seemingly locked doors that can't be opened, you walk through them, upgrading your sword is optional, (and can't even be done until AFTER one of the major bosses, while in the original game, you're required to have the Master Sword before that part) and the sheer challenge of the dungeons make this game unbelievably difficult!
I highly recommend this hack and prove just how hard it really is!
As for Pokemon games, I'd say Ruby Destiiny Life of Guardians provides quite a challenge. The Master 17, the final bosses, and generally the overall game is nice enough to never be too easy for you. Also Light Platinum is very well balanced and can be quite difficult if you choose to avoid trainers and/or level just the starter. Trust me, you really want to be balanced in that game.