In today's world, it has to be Pokemon followed by DBZ. Pikachu is in the Macy's Thanksgiving parade, here. I'm guessing Naruto is third considering the manga's popularity, then Yu-Gi-Oh, and then...Sailor Moon? It had its following in the 90's.
The biggest cult following is probably Ghost in the Shell. Even when I was a newbie to anime, I at least knew the name.
I have no illusions that this is all conjecture. Until somebody actually does a poll testing name recognition......also, it doesn't seem so easy to me to compare the popularity of a series in the last generation to popularity today. I mean, comparing some of these is almost like comparing Thundercats or GI Joe to Avatar or Spongebob.