In my experience geographic separation is usually used for flights operating visually and can be really useful for handling Special VFR flights - clearance such as one aircraft holding to the E of one point and another to the W of another point can be used to ensure the aircraft are never closer than the distance between the two points (I hope I don't need to draw a picture to show the relative positions of the points and aircraft!).
Deemed separation can be used for both visual and instrument flights and is applied when there is no suitable (or convenient) separation in Doc 4444 but the relevant authority is content that either there's no possibility that the aeroplanes will bang into each other or it satisfies some legal nicety (c.f. aircraft inside CAS are deemed separated from those outside CAS).
Certainly used this way in the past in the UK and I've seen similar principles applied elsewhere.