Omens of the Derp sounds very similar to the Cthulhu expansion of the mobile version of the game. Omens of the Pharaoh is similar to the Dark Pharaoh. Pretty cool.
Either Omens of the Deep or Omens of the Pharaoh. Gates of Arkham is harder, IMO. Brutal at times. Although all of the expansions are harder than the base game. Between the other two, I would choose based on whether or not you want to add skills or relics to the game. If you're still undecided, I would choose the theme / setting that suits you better.