Considering half of my GBA and DS collection is made up of underraited titles, that nobody seems to care about (and most of my home console titles are made up of (mostly) popular titles, so yeah). So I'll just name a few from various consoles:
Monster Rancher 2 (PSX)
I do belive not everyone was a fan of Monster Rancher at the time, and thought it was a Poke'clone on the PSX, kinda like Digimon was on the DS (and predecessors on diffrent consoles before it), it actually plays more like an arcade breeder. You raise you lone monster, freeze it, fuse it to create a stronger one (depending of the stats of each parent) or just to show off your own Mr. Badass.
Battle system was more fun, as you had more control of your monster too. the Left and Right analog sticks control the monster's basic movements, the X, Triangle, Square, and Circle buttons have the attacks, rather than letting the menu do all the work on a tiny screen.
Namco Musem (Multi-Platform)
While this gallery of games is Namco's way of saying "In Ya Face, 'Foo!" and most of the time was ignored, I kinda bought a few ports, and boy, each version had it's own set of extra games other than the big guns. You got Mappy, Toypop, and other [parasitic bomb] that nobody cared about, but it was on a disk so it was a very big deal, same with the GBA port of Xevious. Namco, we love ya.
Shadow the Hedgehog (Multi-Platform, again.)
Now I might be the only one who can tolerate (most) Sonic games, and this one pissed me off quite a bit, but I do say the silver lining to this game was the multi-player that nobody even knew about. Even though the GCN and PC multiplayer was vastly superior to the PS2 version, but for me, the PS2 version had a little more response than the most of 'em.
Super Robot Wars OG1 + 2 (GBA)
While the Super Robot Wars franchise was huge in japan, a small rebel force penetraited the sheild generaitor and landed on US soil, it wasn't very popular due to it starting out sometime in the handheld's lifespan (along with MAJOR GBA titles coming out) and licensing drama, but it had a cult following outside the US, which resulted of the Endless Frontier series to be brought over to the US.
Sonic Pinball Party (GBA)
Even though I own a copy through a compilation pak, it's pinball. and I am a fan, I'll admit. Tricky stages, challenging modes, and the Tiny Chao Garden made this one a classic for me (others had Sonic Advance and whatnot, while this title was mostly ignored without the two-pack, and I was in elementary BTW when the game first came out) when I got it used.
Jurassic Park (SEGA)
Now THIS is how a movie licensed title should be made. While it has bugs here and there, by far it's one of the best out there, yet overlooked at the same time. Playing as a Velociraptor was teh shiz. Why play Grant when you can play the guy that's trying to KILL him? Yeeahh.
Rocket Knight Adventures (SEGA)
While it may be viewed as a Sonic clone on the cover, but you know what they say, sometimes you just can't judge a book by it's cover. It's Konami, the king of TV show license based arcade games. While it was a platformer, it felt arcad-y at the same time,
with the story progressing at the same time while you are playing the game.
Being a kamikaze knight has never been so much fun.
While these are SOME of the games I own in my large collection, but boy, I had fun playin' them.