[thejeff]

Atlantis is definitely the Lovecraftian version. Deep Ones are out of Shadow over Innsmouth and probably other places. I think the Atlantis connection is not from Lovecraft. More just a water based name, I guess.

EA Ry'leh is not directly related to the other two, though they have the same types of powers and empire. The Aboleths were destroyed by the falling star that brought the Illithid.
Oddly, other than the name and some of the void creatures, R'lyeh has less direct connection to Lovecraft. Both Aboleths and Illithids are D&D monsters. Definitely inspired by, but not directly from the Cthulhu Mythos.