NON-popular is a little vague, OP. Are we talking raw sales figures, fan devotion, being a popular scapegoat, being a lesser-known IP (internationally, at least), or something else? Ah well. Here are a few I play regularly that might qualify for different reasons:
Nier (PS3)--brightly lit, often colorful, very funny, and absolutely grimdark story and action
Hunted: The Demon's Forge (PS3)--not too deep but still fun fantasy action, has characters and a world with enough substance to develop in further games (but inXile and Bethesda won't do it), really enjoyable voice acting
Mystery Dungeon 2: Shiren the Wanderer (DS)--an outstanding console roguelike, remake of a SNES-era game with great graphics and music, no franchise baggage weighing down its gameplay (unlike Pokemon)
Final Fantasy III (DS)--a little clumsy in its use of DS-specific features, but very playable, nice story and graphics
Monster Hunter Freedom Unite (PSP)--popular in Japan, but I don't live in Japan
Tenchu: Shadow Assassins (PSP)--takes the story in an interesting direction, controls adapted rather well to the PSP, and there's still all the usual funny, quirky, and messy stealth action of the series
Thief series (PC)--all the challenge and silliness of Tenchu plus a steampunk aesthetic and Benny the Guard, extremely popular in its day but it's an older franchise now (GOG has all three games for a good price)
Risen (PC)--fans of Gothic know it and Risen 2 released recently, but it's a unique take on the Western fantasy rpg genre (mechanics as well as story/setting) and a nice change from Tolkien/D&D-inspired stuff
Nier (PS3)--brightly lit, often colorful, very funny, and absolutely grimdark story and action
Hunted: The Demon's Forge (PS3)--not too deep but still fun fantasy action, has characters and a world with enough substance to develop in further games (but inXile and Bethesda won't do it), really enjoyable voice acting
Mystery Dungeon 2: Shiren the Wanderer (DS)--an outstanding console roguelike, remake of a SNES-era game with great graphics and music, no franchise baggage weighing down its gameplay (unlike Pokemon)
Final Fantasy III (DS)--a little clumsy in its use of DS-specific features, but very playable, nice story and graphics
Monster Hunter Freedom Unite (PSP)--popular in Japan, but I don't live in Japan
Tenchu: Shadow Assassins (PSP)--takes the story in an interesting direction, controls adapted rather well to the PSP, and there's still all the usual funny, quirky, and messy stealth action of the series
Thief series (PC)--all the challenge and silliness of Tenchu plus a steampunk aesthetic and Benny the Guard, extremely popular in its day but it's an older franchise now (GOG has all three games for a good price)
Risen (PC)--fans of Gothic know it and Risen 2 released recently, but it's a unique take on the Western fantasy rpg genre (mechanics as well as story/setting) and a nice change from Tolkien/D&D-inspired stuff