You can count on the direction of the last answer as a positive suggestion. If you work with a high salt environment or a high acid environment (low pH) you should consider Halobacterium or Sulfolobus respectively. The methanogens (Euryarchaeota) are strictly anaeroabic, something that puts constraints on their use. I would vote for Sulfolobus because it has a more typical irregular lobed shape morphology, the typical subunit cell wall and an archaeal membrane structure (not a bilayer). This morphology is different from Halobacterium, which also has a typical subunit wall. Halobacterium is rod shaped like many bacteria. The irregular lobed sphere shape and subunit wall are uniquely archaeal and highly characteristic of the domain. But in the end it depends on your specific direction and as stated above your interests.

Hi Ron, The above suggestions are great. Halophiles are definitely easier to use vs methanogens and thermophiles. The question is in the choice of halophiles. Haloferax volcanii is a great system to work with because it has genetic system worked out. Halobacterium halobium has a lot of transposition. The question is what is the goal of your project before you start out on your choice of the Archaeon.  

thanks everyone for your responses!  I see that archaea have several tractable systems, but vary in their make up enough that you need to really find the system closest to what you want.  I'm doing a bioinformatics exercise with some genomes, so I had some freedom to choose.