Atari sounds are found in commercials and movies because they are legally owned by the Warner Brothers sound archive. They were created by Atari in the early 80's (while owned by Warner's). They are therefore fully licensed when you hear them. I would suggest contacting Warner Bros. to find out about usage. If the game you want to sample isn't from Atari, check to see if the company is still around. Activision holds rights to their own games as well as Absolute and Imagic. All old M Network/Mattel/INTV games for the 2600 are owned by Intellivision Productions or Telegames.
RE: Atari sounds sample rights