I'd say Dawn War pantheon is my favorite as a pantheon because of the Dawn War history and the Cosmology. 4e did a great job here.
Golarion probably has my favorite individual deities to use and build world elements around.
I like a lot of pantheons in my D&D.
I am very familiar with and enjoy a lot of the Greyhawk and Forgotten Realms pantheons, and a bunch of Dragonlance's pantheon.
Cthulhu Mythos, Stormbringer Courts of Chaos, and the Chaos pantheon of Warhammer appeal to me a lot as well. Conan's Hyperborea with Marvel serpent Set, Crom, and others are great too.
I like Eberron's mix of religions, particularly the druid factions, the Blood of Vol, the Dragon cults, the Silver Flame, and the Dark Six, but I can never remember the individuals of the Sovereign host, they blur together in my head and never really stood out beyond the amorphous host.
I really like the
Book of Fiends from Green Ronin for evil archfiend deities, but
Book of the Righteous always left me cold other than the Asmodeus story part of it and the gods there blur for me as well.
Birthright's pantheon never grabbed me much either.
I particularly like Lothian and the Holy Lothian Empire from
Ptolus, but the rest of the pantheon (with a few exceptions like Father Claw and Gaen) leaves me pretty cold. Lothianism is a great way to have a mono/henotheistic sort of medieval church in polytheistic D&D, and a great way to incorporate a bunch of other elements I like in through saints or the displaced Old Gods.
Scarred Lands' Pantheon with its titans and gods is a very D&Dified Greek titanomachy that works well and has a ton of story and flavor potential that reached deep through a lot of the Scarred Lands in great ways.
D&D has also done pretty well with real world Norse, Greek, Egyptian, Babylonian and other pantheons in various versions of
Deities and Demigods and third party things like
Lore of the Gods.