I've been giving this some more thought, and I'll say that my favorite series is a tie between Zelda ad Pokemon.
Zelda has my top 3 favorite games of all time in its franchise and a bunch of others that I really, really like as well, but it also has some that are either just alright or in one case a steaming pile of tripe. Pokemon, on the other hand, has consistently produced stellar games (main series, anyway - I don't keep up with any of the side stuff) and I value each of the games generation-to-generation about equally. Plus I actually get more hardcore with Pokemon than I do Zelda, having put upwards of 1000 hours into the games over time.
So yeah, they're both about equal to me.
After those two, probably Metroid.