[Lalaith]

I don't think that Tolkien did, other than perhaps in Tom Bombadil's comment about "the dark when it was fearless", portray a prelapsarian Arda. (Of course, I'm going by the Sil here and he may well have written other versions, so maybe HoME readers can prove me wrong) But in the Sil, Arda was marred by Melkor before any sentient life appeared.
I always assumed the Maia who joined Melkor = Fall of the Angels.

Atlantis/Numenor, of course, but what about parallels between Numenor and the Flood?
(I must say, I agree with the reservations davem and others have expressed about Adam and Eve and the serpent, but what I find really difficult getting to grips with, is the Flood. Even if we could accept that all humanity, even new born babies, were irredeemably evil, except for Noah and co, what about all the animals? Did they have moral sense and thus commit evil and deserve to die?)

Re Tolkienian deluges, it's not just Numenor of course. The breaking of Arda during the Valar-Melkor battle must have involved thousands of innocents perishing.