There are a few i can think of readily. Tezcatlipoca (main Aztec deity) looks like some strange spaceman, and also seems to have the end of one of his legs chopped off and replaced by some tentacles. Baphomet has a strange shape. Various ancient Egyptian gods were rather monstrous in form 
And some trivia:
There was said to exist in classical-era central Athens, near the main Stoa, a path of three converging roads over which there had been erected a statue of Hermes, which either had three or four heads. This is mentioned both in concurrent texts (a comedy by Aristophanes makes fun of the statue) and in the massive work of Photius, in the 9th century AD, titled Bibliotheke, or Myriobiblos (Photius Biblioteca in latin).
In the Biblioteca it is also noted that the statue had the name of "Hermes four-headed (or four-ended), seer of all". It is supposed that each head was directed at one of the forking paths


And some trivia:
There was said to exist in classical-era central Athens, near the main Stoa, a path of three converging roads over which there had been erected a statue of Hermes, which either had three or four heads. This is mentioned both in concurrent texts (a comedy by Aristophanes makes fun of the statue) and in the massive work of Photius, in the 9th century AD, titled Bibliotheke, or Myriobiblos (Photius Biblioteca in latin).
In the Biblioteca it is also noted that the statue had the name of "Hermes four-headed (or four-ended), seer of all". It is supposed that each head was directed at one of the forking paths
