I will throw in two minis - Blast Off (PSN) and Archibald's Adventures (PSP, Win, MAC, iPhone).

Not sure about Ninety Nine Nights but agree with Eternal Sonata and Crackdown.  Have heard good things about Enslaved and have Deadly Premoniton in my backlog probably going to like it since I really liked D4.

I'll write the reasons why it wasn't likely considered a gem, followed by why I think it is.

Enslaved... The gameplay was mediocre, but the art design and story was fantastic. It's a great experience, that lacks good gameplay, but the gameplay was good enough to not get in the way, and sometimes that's fine.

Pandora's Tower... The gameplay was mediocre, same as above.

Lightning Returns... The story was stupid with terrible dialogue. though it was probably the most thematically interesting JRPG last gen aside from Xillia 2, (it was just written extremely poorly) , the graphics were horrid, but the game was bloody awesome, with a lot of interesting mechanics that spanked the hell out of most other JRPG's (except Xenoblade and Xillia 2 last gen for me). It's was really fun theory crafting different viable builds, that played completely different.

Xillia 2. Best JRPG story last gen,  with a top knotch battle system, and it doesn't really get treated like that imo. Terribly boring world design, Reusing the world wouldn't be bad if it was interesting, but reusing most of the same boring world is bad. However, it was an RPG with a great story, and great gameplay. 

Vanquish (360/PS3)
MadWorld (Wii)
Muramasa: The Demon Blade (Wii)
No More Heroes/No More Heroes 2 (Wii)
Sin and Punishment: Star Successor (Wii)
Radiant Historia (DS)

Zak and Wiki -Wii
Mercury meltdown madness -Wii
Excite Truck -Wii
Disaster day of crisis -Wii
Lost in shadow -Wii
Heatseeker -Wii
Medal of honour heroes 2 -Wii
Cursed Mountain -Wii
Deadly creatures -Wii
Obscure 2 the aftermath -Wii
Ghost squad -Wii

El shaddai, Majin and the forsaken kingdom. Glad to see Spec ops on peoples list too one of my favorites from last gen.

Bastion.
To The Moon.

Alice: Madness Returns.
Alone In The Dark: Inferno.
Siren: Blood Curse.
Enslaved.
Spec Ops: The Line.
Murdered: Soul Suspect.

Battalion Wars II

Enslaved: Odyssey to the West
Radiant Historia (Got a decent amount of attention when people voted on a second reprint, but still relatively unknown)
A couple people have already beaten me to Lost Odyssey, it looks like.
Also, I thought Kameo: Elements of Power was great. A shame the sequel didn't pan out.