For me, TOS will always have the top spot, partly because that's the Trek I first fell in love with.
My preference for the shows is more emotion based than academic (plot, effects, etc). For a series to make an impression on me, I have to grow to love at least some of the characters. All the shows had merit, I didn't find any of them awful, but if I didn't fall in love with the characters pretty soon, then it didn't become a favorite.
After TOS, I liked TNG and VOY the most, and I while I did enjoy watching DS9, I was never deeply into it. Same with Enterprise, it wasn't unpleasant to watch but the characters didn't affect me on an emotional level, so both it and DS9 rank lower in my personal list.