The convention is to use the label of the "marked" feature. What exactly that means varies from theory to theory, of course, but at minimum it implies some kind of (usually phonotactic though at least perceptual) salience. I'm not sure exactly what you mean by "most likely" to be positive or negative. Are you talking about corpus frequency distributions? That's not really a mainstream analysis.
As far as examples go, I'd have to look them up. Off the top of my head, I believe several of the Athabaskan languages with small vowel inventories use a binary distinction with [front] marked.