I wold have suggested Vinland Saga, but since it's already mentioned, I can't think of anything in particular. Countless series draw some inspiration form either of those mythologies, be it names, terms or ideas, but relatively few can be said to be based on them...
Eigi man ek þá lǫg jómsvikinga ef ek kviði við bana eða mæla ek æðruorð. Eitt sinn skal hverr deyja
Atlantis plays a role in the background story of the Escaflowne TV series, and a few scenes occur there. But it's a somewhat stylized version of Atlantis, which may not match descriptions of Atlantis found in classical mythology.
EDIT: Oops, I missed that you were asking for manga... not sure if the Escaflowne manga includes Atlantis or not.
Edit, just to clarify: Some of this list is more "based upon or references frequently" rather than "actual setting"
Norsewise: Oh my Goddess! Matantei Loki and Matantei Loki Ragnarok Valkyrie Profile manga (based on the game) should be based on norse mythology by default. Quite a few of them have been scanlated so you stand a good chance of finding them. Akai Tsurugi (The Scarlet Sword) by Ryo Azumi (Although its not on MAL, and BakaUpdates doesn't have any scanlations listed so that might not be so easy. The first link has a transcript for an exerpt that can be read on the mangakas website though)
Shishi no gotoku (Like the Lion) from the same author is about this guy according to the wikipedia page on Ryo Azumi. I'd never heard of it though :( Harlock Saga: Nibelung No Yubiwa by Leiji Matsumoto. More info on wiki although that also talks about the OVA series.
Der Ring des Nibelungen by Riyoko Ikeda (of Rose of Versailles fame) ... although again, I can't seem to find much info about it past the cover pictures I'd already seen (YesAsia would show you them, at least) x_x
Greekwise: thats harder :|
Sharkall already mentioned Historie, but I'll second it.
Past that, the only one I can think of at the moment is the manhwa Legend of Nereid.
For the most part, I think it is just name referencing, yes.
I am, however, sure I've read certain chapters/stories within it where the mythology comes into play far more than in the others. Unfortunately all my old dark horse omg volumes are boxed up so I can't check for specifics :(