Beyond Two Souls is hands down the best looking sub HD console game ...

Muramasa, Kingdom Hearts 2

I don't think you should divide the 2. There's sub hd games that look better than hd games.

Metroid Prime

A 2.35:1 movie presented in 720p is still called HD, Beyond two souls doesn't qualify.

Zalda windwaker on GC is the best looking sub HD console game.

What resolution does it run at? And source?

Okami

What you're saying makes no sense ... Beyond Two Souls resolution is 540x1280 which is a far cry from the standard 720x1280 HD resolution. 

http://gearnuke.com/new-interview-david-cage-hints-strongly-beyond-two-souls-playstation-4/

This interview shows that Beyond Two Souls was targetting at a resolution of 720p but if we go by the gameplay you'll notice black bars and the evident aliasing doesn't help hide that the game is of a sub-HD resolution. 

The game likely runs at a ballpark of 540x1280. 

So we can only guess at the actual resolution, but a 720p window minus black bars means sub-HD, that makes sense to me.

Kind of like The Order 1886 running at 800x1920.

Explains how they were able to get such impressive graphics out of the PS3 hardware.