I was going to refrain from listing Earthbound, but since Magnus brought it up I'll comment. Earthbound being overlooked is still the reason why we don't have the MOTHER 1+2 remake and MOTHER 3. This is a game that wasn't overlooked because it lacked advertisements. The only logical answer as to why it was overlooked is because it was an RPG in an era where Americans just weren't all that interested in RPGs that weren't named Final Fantasy. Nintendo advertised the hell out of that game. It was everywhere, Nintendo Power published God knows how much stuff on it. And, for all those gamers who didn't want a hard RPG they couldn't figure out Nintendo was nice enough to sell you the player's guide with the game. Because of this, the game came in a huge box (about as big as a Wii). The box was yellow and bright and shining and had a giant Starman on it. There was no way you could walk into a store and not see this game.
Despite all their efforts, the game simply didn't sell and now here we are over 15 years later and the people who did play the game are still begging for the others while Nintendo says "but you didn't want them last time".
Mischief Makers was definitely overlooked. It's not my favorite game and I haven't played through it extensively, but it was fun and I will never forget "shake shake shake".
I'd like to add another reason games go overlooked - not even production. And I believe there is one company that fits this category perfectly. They happen to be my favorite third party: Atlus. They publish absolutely brilliant games, but they never make enough of them. So, they get overlooked because only 10 people get to actually own each game. Games like Riviera, and OgreBattle 64, and there are tons of others. Basically every game they make. I've never played an Atlus game I didn't like.
And to take a step into the past, the Lufia series of RPGs terribly overlooked. The two recent games (one for GBC and one for GBA) are not all that wonderful, so I'm not really concerned about them being overlooked. But the first two SNES games have a brilliant storyline and characters that are engraved in my head forever. A wonderful soundtrack. And a unique puzzle dungeon setup. They are just good games, plain and simple. I'm sure Terrisus can tell you all about Lufia 1. As for me, I prefer Lufia 2.
The Soul Blazer Trilogy (Soul Blazer, Illusion of Gaia, & Terranigma) was also overlooked. Terranigma has the excuse of never being released in America (but Europe got it). So, as such, I have never played it (although I've highly considered picking up a ROM; I only do that under extreme circumstances because I'd rather buy the games). However, I own the other two games and they are both great (although I much prefer Illusion of Gaia). They are action RPGs and they are fun. And you've never heard of them.
Next, another game that probably only Terrisus and I have played: Mario Clash. There's a really easy explanation as to why this was overlooked: It's a Virtual Boy game. Think old school Mario Bros with the Pow Block except in 3Dish. I'm still waiting for a follow up game. If this hadn't been on the Virtual Boy, I think it would have been very popular. Nowadays, an online multiplayer mode wouldn't be so bad either.
That is all I have for right now I suppose. Perhaps I'll add more if I think of them later.
EDIT ONE MINUTE LATER: Trace Memory. It's a genre that not everyone will enjoy, but I found this game absolutely fascinating. It's amazing to me how I meet people who love Hotel Dusk that never played Trace Memory or don't like it. I have one friend who adores Hotel Dusk, but when I handed him Trace Memory to give a shot he was sick of it before the intro was over.
