Halo: Reach Guide

Yes, Master Chief, the star of the previous Halo games, can be seen in a stasis chamber during the final cutscene in the The Pillar of Autumn mission. After manning the AA gun and destroying the Covenant Corvette ship, a cutscene will show the Pillar of Autumn taking off. A shot from the interior of a ship's cargo hold will then appear. At this moment, begin tapping the RIGHT ANALOG STICK to the right. If you tap it at the right time, the camera will pan to the right side of the cargo hold and you can see Master Chief in Stasis.

According to the Legendary Edition commentary, Jun is still alive at the end of Reach. He is probably safe in Dr. Halsey's lab -- she survived as well. Perhaps downloadable content will explore their fates.