Blender saves a new file every time When I click save or hit Command + S what appears to be a new version of the document is created. So if I save 2 times, I get 2 documents, filename.blend1 and filename.blend2.

What exactly are these files and why is Blender creating them?
These are backup files created by Blender and are fairly normal.

Excerpt from the wiki


  Save and Auto Save
  
  ...To reduce the chance of
  losing files when those events occur, Blender can use an Autosave
  function. The File tab of the User Preferences window allows you to
  configure the two ways that Blender provides for you to regress to a
  previous version of your work...