I think SPD 3 is working on Mario vs Donkey Kong. 

lol apparently now.  I think it should be fixed for now though.  Im going to leave Smash Bros under Namco Bandai for the moment.  Ill look up some info on it and see if they came back because from the link above it does say they arent together anymore

SMT x Fire Emblem and Devil's Third.

edit: Starfox and Metroid.

I'm positive there are more second parties out there. I think Kirby and the Rainbow Curse is. 

I'm typing them when I think them.

edit: Yarn Yoshi (Good-Feel & Nintendo SPD)

        Devil's Third (Valhalla & Nintendo SPD)

Do you all know what teams by any chance?

Tagging.

To OP: This might help you. Its from old post and doesnt have sucker punch in the list.

Naughty Dog: Uncharted 4, TLOU second team game.

Sony Bend: Horror game.

Guerrilla Games: RPG game.

Guerrilla Campridge: Unknown PS4 game.

Sony Santa Monica: Either god of war or new IP.

Media Molecule: Unanounced PS4 game.

Sucker Punch: New IP or next Infamous.

London Studio: Unanounced PS4 game.

Japan Studio: Unanounced PS4 game + Freedom wars + Support.

Polyphony: GT7 probably.

Evolution: Driveclub.

SCE san diego: MLB series.

Quantic Dream (second party): Unanounced PS4 game.

Ready at dawn (second party): The order 1886.

SEGA: Yakuza series.

Capcom: Deep down.

Sanzaru games: Status unknown.

Supermassive Games: Until dawn.

Other exclusives: Rime, Wild, Everybody has gone to rapture etc.

http://gamrconnect.vgchartz.com/post.php?id=6591159

Under Nintendo you should add Hal Laboratories, who usually makes Kirby games. So right now they are making Kirby and the Rainbow Curse.

Also S.T.E.A.M. and SMTxFE should be under Intelligent Systems.

There should also be Genius Sonority, though we don't know what they are making. 

This thread is a good idea though!

In case you missed above.

Yarn Yoshi (Good-Feel & Nintendo SPD)
Devil's Third (Valhalla & Nintendo SPD)