You're mean for throwing the "all time" clause. I prefer ratings by genre personally.
#1: Angel Beats. Content Per episode is top tier, characters have depth and are believable, outstanding music, best open ended anime ending ever.
#2: Eureka 7 Psalm of the Planets: First Shounen coming of age series I watched, still my favorite. Sorry Evangelion fans, but Renton is a mc that doesn't make me want to cut myself
#3: Trigun. Try to tell me you don't love Vash. I'll cut you, I swear.
#4: Toradora!. And to think at some point I didn't care for romance/dramas.
#5: Welcome to the NHK. If you haven't seen it, do so now.
I don't rank series that are incomplete(Naruto, OP, Bleach, Fairy Tail get benched), and I severely downrank series that grossly overplay certain elements (fanservice, muscles, gore, idiocy). Top anime are those that can cover the whole emotional spectrum, have an engaging cast of characters, simple but effective art (music quality is a plus), and have a good Opening episode(s) and closing.
Honorable Mention to:
Persona 4 the Animation for having the best main character based off a silent protagonist in a video game.
Cowboy Bebop for Best English Dubbed series I've watched.
Dragon Ball for convincing me in my childhood that Japan was just fucking awesome