Best potion system ever is in Path of Exile.
Basically, potions are items that you place on your belt. Now, here's the important distinction: They're not consumables, they're regular items, and you can have maximum of 5 of them. Now, how is that a good thing you ask? Every potion is a flask filled with a certain substance - there are normal potions, that refill certain ammount of health / mana on use, so let's use those for our example.
You see a red flask on your belt. All good. You press 1 when your health drops and it gets refilled on basis of how efficient the flask is. Standard so far. Buut, your flask doesn't disappear on use - instead, it gets a bit emptier and loses charge, and after certain ammount of uses, you have an empty flask that you can't use in your belt. So, how do you refill them? By killing enemies, naturally. Now, let's get to how is it all interesting: Beside normal flasks, you can get magical, rare and even unique ones, which grant you certain effects on use, like, for instance, that 50% of health regained on use is transferred to your minions - and there's loads of effects like this. And beside health, mana, and 'both' potions, you also have special ones - potions which don't refill your health at all, but, for instance, grant you guaranteed critical hits for the next two seconds.
So basically, it turns potions into items which you will collect, compare and look for, it prevents them from being spammed (when you're fighting a boss, there's only so few enemies you can kill,) and it generally makes them more rewarding to use.
Path of Exile indeed is the best system, it rewards you for smart play, the flasks themselves have itemization value, the potions do different things, spam-quaffing potions is usually not rewarded, and basically you refill by killing. It's literally every good idea anyone ever had regarding health potions.