Halo (and its sequels) are other Bungie games containing references to Marathon.
The Forerunners of Halo are very similar to the Jjaro of the Marathon Trilogy. The Forerunners, however, play a major part in the plot, as opposed to the background role taken by the Jjaro.
Master Chief,protagonist of the Halo Series
Apart from the references (including repeated appearances by the Marathon logo), shared game developer, and other minor similarities, Halo and Marathon don't have much in common. Some similarities include the mention of Rampancy, and, in Halo: 3, terminals. However in Halo: 3 the terminals are from the Forerunners, not they player's superiors, and unlock an achievment called Marathon Man -- an obvious reference to Marathon.