What types of archaea have been found in animals?
Humans:

A pioneering study using 16S RNA primers found only Methanobrevibacter smithii in the human intestine.


  Eckburg PB et al. (2005) Diversity of the human intestinal microbial flora. Science 308 1635-1638


In a recent review there is a comprehensive Table of archaea found in humans (this includes non-intestinal flora):


  Dridi B et al. (2011) Archea as emerging organisms in complex human microbiomes. Anaerob2 17: 56-63


Much of the work that is catalogued by Dridi et al. is repeated identifications of Methanobacteriales (Methanobrevibacter smithii, Methanosphaera stadtmanae and Methanobrevibacter oralis), but there are others from the Thermoplasmateles, the Halobacteriales and the Sulfolobales, plus some that are thought to be members of unknown archaeal orders.