Favorite NPC? Interesting. I'm going to go break this down by game...
Although technically Kafei can't really be called a Non-Playable Character since you actually do play as him at one point during the Anju/Kafei Sidequest, I would definitely consider him a personal favorite, due to a combination of care for his character and heart-moving plight, as well as his overall character design. The Zelda series doesn't seem to have very many strong-hearted male characters that come in the same vein as Link himself, which I think Kafei was a rare example of; I would actually love to see more male characters in the series akin to Link and Kafei.
I also really liked Cremia in Majora's Mask for some odd reason, even though I hadn't been particularly fond of Malon in Ocarina of Time.
Wind Waker, my favorites require me to mention Tetra and her snarky attitude, as well as Fado who although didn't appear very much, seemed like just the character I would've liked had he been featured more.
I actually think that my Absolute Favorite NPC just might be Linebeck though, with his laughable demeanor yet touching character development. Groose in Skyward Sword was pretty impressive too, but there's something about Linebeck that puts him on another level to me. Perhaps it was something about the combination of the rambunctious young Link traveling ALA partner-in-crime alongside captain Linebeck, an unlikely pair ravaging the seas...just a concept that just resonated with me.
Zelda in Spirit Tracks was also technically playable as with Kafei, but I also can't neglect to mention her as I really found her character to be fantastic--she might perhaps even be my favorite incarnation of Zelda in the series. To me, she was the perfect blend of kind-hearted and sweet alongside feisty attitude and spunk. Yes, she really might be my favorite...
I'd now like to mention Queen Rutela whose character I found to be bittersweet yet lovely, Marin from LA whose character I found beautiful and also was someone I felt I identified a bit with personally (why she holds my avatar), soft-hearted Nayru from Oracle of Ages and perhaps Ralph (Actually I do think he's one of the rare characters of the series to fit with Kafei and Link), and oh, most absolutely definitely Maple, who I find to be such a memorable character that seems to often go unmentioned and unnoticed, much like the Oracle series in general actually. She's comical to ram into and steal stuff from, as well as just a really interesting and likable side character. It's just too bad she slips the radar so much...
Lastly I'm going to give a shout-out to Navi, who defying all the internet hate for her, just happens to be my personal favorite sidekick.