For me, it depends on both the price, and how quickly I think I am going to use it up. 50ml bottles make more sense from the point of view of oxidation, you'll finish the bottle way before it "goes off". They are also easier to take with you when you travel. If you are blind buying, they make more sense, especially when in the UK where I live a 50ml bottle and a small sample decanted by a 3rd party cost about the same. And I know this probably doesn't mean much, but they feel better in the hand.
Yes, 100ml bottles do tend to be a better deal. I'm not sure what my "cut off point" is where the cost savings of a 100ml bottle outweigh my normal preference for a 50ml bottle.