Yes I often substitute one for the other: yoghurt has more tendency to split in sauces, or be a bit watery (probably not Total0% though),
quark can be a bit 'grainier' than FF (in Tofu cream for example). FF and Quark are generally milder in taste than yoghurt which tends to be a bit sharper (maybe that's just my home made variety!). But yes running out of one does not mean you have to run to the shops as long as you still have on of the others.