Steambot Chronicles. I absolutely loved this game. It had it's flaws, but it was charming as fuck. But it isn't that popular. It was popular enough to get a PSP sequel that was...okay, I guess. But a true PS3 sequel was cancelled because of lack of interest.
And despite how much tumblr latched onto it, I really enjoy the DanganRonpa series. It's just the right combination of Phoenix Wright and anime that I can't help but really enjoy it. I do kinda wish I could make it a lot harder than it actually is. And while it has gotten some good attention, it's not popular with anyone outside of tumblr, and people who like Phoenix Wright inspired games.
Harvest Moon. It's a game series about farming, talking to people, farming, building relationships, farming, getting married, farming, having a child or two, farming, saving the land by restoring power to a goddess of some kind, farming, dying, your child taking over, and then ever more farming.
Way of the Samurai. I really enjoyed the first three games of this series, and I KINDA liked the fourth. Admittedly I haven't played much of the fourth. And it wouldn't be listed if it weren't getting as much attention as I wish it was.