Rufus SPOILERS!!!!!!!! Enter at your own risk.

[Mercen-X]

Tseng

Elena implies fairly heavily that Tseng died when she confronts Cloud at Icicle Inn.

The fact that Tseng doesn't appear for the rest of the game also supports the supposition that he died. It's not impossible for SE to bring him back, but, unless they do, his fate is fairly apparent.

Scarlet and Heidegger

We don't actually see them die, although it's a logical assumption given the power of the blast that marked the end of the Proud Clod.

sub crew

The sub crew is probably too insignificant to be mentioned either way, but I would suspect that SE leaves them alive if the issue is addressed.

Hojo

Given that Hojo completely disappeared from atop the Sister Ray, it's safe to assume that he died.

Dyne

Dyne should be assumed dead until he actually returns.

Did you know the Proud Clod was going to be called Proud Clad? I think that sounds better.