Honorable Mentions that are niche, but anyone browsing forums or chans knows almost certainly knows about
>Mr. Gimmick!
>Little Samson (Lickle: Legend of the Holy Bells)
>Dark Cloud
>God Hand (Or anything by Clover Studios)
>Hylics
>Ghost Trick
And there's probably some I missed, but those are the ones I happen to see people talking about fairly often.
>Haunted Mansion
Although the story and dialogue is cheesy and very "gamey" at times, the puzzles and mechanic quirks are phenomenal. It plays sort of like a "reverse" Luigi's Mansion where more emphasis is put on the environments rather than the characters. And rather than combat, there's more puzzles as you have to turn on the lights before being able to capture friendly ghosts that come out, which leads to pretty interesting situations as you have to figure out how to clear a room first. It's also worth noting, it's not based on the movie what-so-ever, it's a completely original concept and story. So much so, it seems the game is based off a missing Haunted Mansion cartoon or something, it's very typical Disney and you won't be disappointed if that's your thing. It also adds to the "Spooky 6th Gen Console" games, perhaps a trilogy consisting of Luigi's Mansion, Grabbed by the Ghoulies, and of course, Haunted Mansion. They all play very differently and have their own design quirks, but they're an absolute blast to play around October/Halloween, which is what I did recently.
>Marvelous: Another Treasure Island
It's made by Nintendo themselves, yet I don't ever see this game get talked about all too often even by hardcore Nintendo fan's standards. Mole Mania, StarTropics, Captain Rainbow, even Virtual Boy Wario Land all seem to have more love than this game gets. (By the way, play those games too if you haven't, especially Mole Mania.) It plays much like any Legend of Zelda game, it's the very reason Eiji Aounuma was chosen as director for the Zelda series from then onwards. Instead being a 1:1 Zelda clone, it has more emphasis on puzzles rather than combat and even includes a mechanic similar to point and click adventure games that allow you to search around the environment and click on unknown things or objects or interact with them in other ways. The game is even structured in a way similar to point and click adventure games or a Saturday morning cartoon or even a movie, containing a lot of flashy elements. It has a vibe very similar to the Goonies too, my only gripes with the game is that it's shorter than most Nintendo games and it can get tedious at times. Aside from that, it needs more attention, I'd love it if Nintendo were to revive some of their older series and I think this is one that could benefit.
>Apotheon
Granted, it probably has a following, but I've never seen it talked about here. It's a Metroidvania-esque game that bases it's entire artstyle and setting on ancient Greece. It's only Metroidvania in the sense that you can tackle most tasks you want in whichever order you want, there isn't much backtracking or item powers. The combat is decent, there's little side challenges here and there that spice up the game, but the main appeal lies within the Greek inspirations, setting, and lore. It can drag at times, but if you allow yourself to get invested, it won't be much of a problem.
>Q-Boy
Yes, it's a bootleg, but hear me out. The game happens to be completely original, other than it's artstyle, which happens to be inspired by Kirby. Yes, it is a tad wonky, that's expected of a bootleg. But I'll be damned if it isn't one of the best or most fun bootlegs I have ever played. It also has a mechanic I've never seen in other games, being that your movement and jumps are tied to your attack, use too much of either and you'll be winded. The level design also plays into this and understands this. It's another case of being pleasantly surprised from unexpected situations or "don't judge a book by it's cover." You never really know where a good or fun game can come from until you play it for yourself. It's important to have games like these to remind us again to hold back on our preconceived judgements or assertions.