At least half of the animes mentioned so far are far from being obscure >< Hellsing? Soul Eater? Honestly, people, if you want to write your favorite animes, feel free, but don't call them obscure as well, if they are not. If you want something to qualify as obscure you'd need to have anime fans (like me) to not know it or at least admit they also think it's obscure.
Anyhow, just my opinion. I'd call Ghost in the Shell my favorite, but I don't think it's obscure. The one that does fit both the topic and my taste the most is Seirei no Moribito. it's both marvelously drawn and with a rather well written story and in fact, I had to look for its name by the name of the main heroine
