Sin & Punishment 2 - It's a Treasure game. PlatinumGames and Treasure games always flop.

Tatsunoko vs. Capcom - Default control layout not being comfortable for fighting games, Tatsunoko isn't well known outside Japan, released before Street Fighter 4, music was changed (for worse) in the western release.

Virtua Fighter 5 - Because VF is a substance > style game. Not enought boobs like DOA, not enough flashy stuff to impress teenagers like Tekken, not enough blood or overly violent moves for the the dudebros like Mortal Kombat.

Sorry it took so long...

1. Killzone: Liberation (850,000 copies) -- Killzone: Liberation suffered from a dual injury: low scores and low sales. It deserved neither. It's one of the best games of the seventh generation, and one of the best third-person shooters I've ever played. Perhaps if Liberation had been a first-person shooter like its predecessor and immediate succesors, it would have sold more. Who knows?

2. Zack & Wiki: Quest for Barbaros' Treasure (410,000 copies) -- Despite critical acclaim and a campaign by IGN editors to drum up pre-orders, Zack & Wiki fell flat in terms of sales. I guess a point-and-click adventure game featuring a shirtless boy pirate and golden monkey didn't speak to a mainstream audience. The name probably didn't help either. It's a shame, though, because it's one of the best adventure games ever made.

3. 999: Nine Hours, Nine Persons, Nine Doors (290,000 copies) -- This gem may have gained a substantial cult following but it never found a place in the popular imagination. Lack of advertising probably hurt this game, plus the fact that it's a visual novel. Again, it's a shame, because 999 boasts one of the best video game stories ever written.

4. Patapon (770,000 copies) -- This unique hybird between god game and rhythm game did fairly well considering its unusual premise and mechanics, but it couldn't compete with blockbusters like God of War and Grand Theft Auto.

5. Folklore (280,000 copies) -- Considering the massive popularity of monster hunting/collecting games like Monster Hunter and Pokemon, one would think Folklore would have reached a larger audience. No such luck. Still, very much worth playing.

So much truth in this segment. Your choices aren't either good or bad, you're just choosing the best bad option. This game's story was definitely the best part. I enjoyed the gameplay, but I'd agree it's nothing amazing. Because there's no clear good choice though, it really does reveal a lot about you as a person. This game did make me question my own morals, and no other game has really done that for me either. SPOILERS! The White Phosphorus part was one of the most heart wrenching sequences I've ever played in a game. END SPOILERS!! But yeah, it's a shame this game wasn't more popular. 

1. Vanquish 940.000
Cause you all suck balls for not wanting to enjoy the best action game in recent history.. Sure its short, sure it has no multiplayer.. But my its an awesome experience..

2. folklore 280.000
I actually picked up a second copy for cheap.. Will be a game not to be found easily in the future.. Maybe a bit too wierd for most. The combo linking made it a game you could play in the style you like... Sony didn't greenlight the sequel... -_-"

3. deadly premonition 340.000
Prime example why cutting budgets doesn't work for gamers to notice a game.. Yes it has dreamcast graphics but the story, horror and humor are non to be found in any other game.. A true gem..

DMC3 sold 1.3M. Use official data if you have access to it.

You forgot Lost odyssey -- I think ut just sold 1million + . One of the best Jrpgs and blue dragon which i think its below 1 mil +

And what would you consider official data. You provide no links so am I supposed to just take your word for it. Becides, I see no reason to trust Capcom to tell the truth about anything; especially their own sales figures. We're on the VGChartz forum, I think it's perfectly reasonable to assume the VGChartz database is at least close to accurate. If it's not, well, why the hell are we posting here?!

Official data is Capcom, of course. Who else?

http://www.capcom.co.jp/ir/english/business/million.html

Puppeteer 167,000 hopefully much more with digital but still no where near enough for such an amazing game.
tearaway about 300,000 and possibly double with digital but also not enough for the best game on the vita.

Valkyria Chronicles. According to wikipedia "Valkyria Chronicles has sold over 1 million copies worldwide.[66] It was the 93rd best-selling game in Japan in 2008, selling 141,589 copies. Despite weak initial North American sales, Valkyria Chronicles recovered with sales sharply increasing in April 2009 following a price cut".

For me the art was really great, some cell shading but with a very fine pencil style, design between steam punk and world war 1, colorfull.
In term of game, lots of missions, lots of variety, replayability, characters, weapons. The tactical part is working very well, turned based so you can think about tactic, but also really dynamic with realtime moves and shooting. Good balance between units style, RPG-like improvement of skills, powers to unlock.
I think it's really the perfect adaptation of strategy game for console.