Well, the basic difference that we know of comes in the look of the souls of dead humans and dead eggs-of-kishin. Normal human souls are blue, as with those on Nidhogg in episode 15. The souls of eggs-of-kishin (Jack the Ripper, for eg) are red.
Simply put: blue = good, red = bad.
Now, the colours of souls differ for the living characters, some being orange, yellow, or red for e.g. We don't know what, if any, meanings those colours have.
The same is true of the colours Technicians' souls take during Soul Resonance or when they expand their wavelengths in combat.
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