Rune Factory 4

One of my favourite game and game series, really hope there is a sequel, despite the team going bankrupt

The Wonderful 101
Fire Emblem: Radiant Dawn
A-Train (every entry that isn't a broken mess, at least), but I can only speak for the 3DS version :P
Etrian Odyssey (all of it!)
There are a lot of games I'm missing, though.

Pretty much any game that I like.

I guess I will pick the top game that didn't make 1m from my top 50 list.

Romance of the Three Kingdoms IX, but this goes for RoTK VII, VIII, X, XIII as well.

"Eternal Darkness" barely passed 200k. That was an amazing game.

In the list of games I regret never playing, that's one of the highest.

Metroid Zero Mission

Well as a 7 and 8 fan I really hated it at first as it was ruler only. But after multiple attempts at trying to like the game a bit more it grew on me. The worst mechanic of the game was barbarians, if you bordered them you lose 3 cities automatically because they start with 300k troops and destory cities in an instant through BSery vs you with 20k  or so at the start. However to circumvent this I beat the game and destroyed them as well, so I unlocked them for play. Then I choose all them, which nerfs them into 100k troops and pretty much a regular force. Then I usually make them surrender to whoever they deserve to be with. Finally with them taken care of we can play the regular ROTK9 game lol. The game has some really good strategy imo and some decent balancing between the 3 kingdoms.

8 was easy once you learned a good strategy and played a decent officer, while 9 is always hard. Agression wasn't annoying like in XIII, and superstar officers can still make the difference. But you can still accomplish a lot with bad officers.

And yeah I rate 10 at the lowest.

For me it's most likely Hogs of War. VGChartz has the game at 0.02M...
http://www.vgchartz.com/gamedb/?name=Hogs+of+War

Bayonetta 2

I think Xenoblade passed one million between Wii and N3DS?

If not, Xenoblade.

If yes, Ico and Psychonauts.