The NES is an interesting console to me in the context of Nintendo's broader hardware catalog because it's a system that is almost entirely carried by the strength of its third party output, with the core in-house Nintendo lineup being on the weaker side as a whole (or at least, pales in comparison to a later SNES incarnation). Rather than get sidetracked by detailing beloved Konami/Capcom/Tecmo classics you've most likely played already, I'll rattle off some of my favorite lesser known offerings for the system:
Faxanadu - Not sure if this game is that obscure but it's certainly not something that makes NES GOAT shortlists even though it curbstomps most comparable games on the system. Absolutely worth playing through.
Crystallis - OP already mentioned this one but I'll reinforce it, quite possibly the best RPG available for the system, exploring the game's world stays exciting for most of its run and there's always some cool arcane secret to discover.
Dragon Fighter - Sidescroller/shooter game, essentially a better version of Altered Beast in its concept and general gameplay.
Gimmick! - Very novel cutsey platformer in which your attack is also your best movement tool. A regular playthrough is easy enough, but the game expects you to fully understand how to utilize the player character's star projectile to their advantage in order to reach hidden bonus areas and unlock the game's true ending.
Gargoyle's Quest II - Fantastic sidescroller stapled onto a bog standard, half-formed RPG that adds nothing to the experience. This isn't enough to drag the game down by much, and the core game is definitely worth a look regardless.