Growing up, Mikey was my favorite. He was so adorable. His cute idiocy and goofyness was totally endearing. My affection for him skyrocketed in the movie because his voice actor was cuteness x100. Mikey will always hold a special place in my heart.
Now that I'm older I find myself more interested in Leo & Raph. Dunno what it is but I suspect that Raphael has that same mystique that Wolverine did for me...his volitile nature and repressed anger makes him dynamic. Leo, for similar reasons actually, it seems like they both hate themselves for not being 'good enough' in their own estimation while being jealous and angry at each other. It's a great combination.