The color of the puddle depends entirely on the angle you are viewing it from. The closer it gets to an 90 degree angle from the ground, the more transparent the water becomes.
Now making the water entirely transparent has the problem of making it also difficult to see what is going on in a 2d environment, since you can't show the player the depressions on the ground. I'd be more inclined to think that it's a discolored spot or a slight depression, rather than a puddle.
I've seen some puddles on a cobblestone street, but depending on the depth the cobbles would naturally peek out of the water at some points. Making the puddle large would make it reasonable to understand it being deeper, since usually streets and others don't have small deep depressions (unless they have been broken for example by the ground frost as is the case here)
Parkerbaby's puddle looks the best out of the options presented here in my opinion, since it has a different texture. Humans pick out texture changes easier than color changes.
I will forever wait for the style of puddle that happened in Pokemon Ruby, where in a certain area you had clouds move in the puddle's reflection. That was a delightful moment, since before that the puddles were mainly a flattish color with a reflection of you if you walked over it.