I wanna say Yoshi's Story, though it seems that it, like SMB2(USA), is starting to come into its own, as all the people who criticized it back when it came out for looking too "kiddy" are now thirteen years older and are becoming more secure in their maturity, and now that we have an actual sequel to Yoshi's Island. I will argue, though, that it's a much harder game than people give it credit for. With six to eight lives at most, and only a single 1-up, hidden rather well, in each level, it's a far cry from the standard Nintendo lives-fest, especially with the prominence of insta-kill obstacles on the last few pages. And it gets really hard if you go for a perfect 30-melon score on all 24 levels (Trial Mode, not Story Mode, is where the game really shines).
Paper Mario is a great game, better in some ways than its sequels (for one, while not as funny of a game, it makes fewer gameplay sacrifices for humor, making it overall a more replayable game than TTYD or SPM), but almost always gets overlooked in favor of its successors. It also gets unfairly panned by SMRPG fans for not being the SMRPG2 they wanted, when it really is. Sure, there's no Geno or Mallow, but if you can get over that and the graphical shift (from 2D 3D on a 2D console to 3D 2D on a 3D console), it works very well as a direct sequel to SMRPG. Bowser forcibly joins Mario's party to get his castle back, they successfully get it back and protect the world from future invasions by Smithy's weapons, Bowser leaves and goes to fix up his castle, Bowser goes to the Star Road intending to discover and possibly steal the Stars' wish-granting power, he gets it and surprises everyone in the Mushroom Kingdom in the middle of a party while they're still celebrating Smithy being defeated. Just assume that the Star Spirits and Star Pieces are the same thing, as are Twink and ♥♪!?, and the two fit together just as well as SML1&2 or SMG1&2. That's not to say I wouldn't still love to see Square make another Mario RPG, of course (seriously, why haven't they gotten on this yet? Nintendo and Square have been friendly for five years now).
Speaking of Super Mario Land 1 and 2, neither of them gets enough love. SML1 is a great spin on SMB, with lots of little twists on classic enemies, all perfectly tuned to a pocket-sized experience (not to mention some nice music), while SML2 is a platforming work of art, with levels that still feel fresh nineteen years later.
The Game & Watch Gallery series really deserves another entry -- and no, the Club Nintendo Collection titles don't count. As I said before, the 3DS would be great for this, using the 3D to subtly simulate the multiple layers inside a G&W screen (backgrounds, foregrounds, liquid crystals in between) and using the camera to simulate a Crystal Screen game.
Mario Hoops is a lot of fun (though I'm still a bit annoyed that they didn't include Geno). Coins, items, and dribbling with the touch screen all work very well. Haven't played it in a while because my DS shoulder buttons always crap out (apparently you're not supposed to put these things in your pockets anymore? Come on, Nintendo. I'm out of college, I'm not going to buy a messenger bag now.).
More later if I remember them.