List of Marathon references in the Halo series
From Halopedia, the Halo wiki
Throughout the Halo series, Bungie have inserted numerous references to their older Marathon series. This is in keeping with their long history of incorporating references and allusions to their previous games in new works. At one point they even revealed that the stories of Pathways into Darkness, their first story based action game, and Marathon were connected in a plot twist. Many of the aforementioned Marathon references in Halo are appearances of the Marathon logo, which, in the Halo universe, is the Forerunner symbol for "Reclaimer".
Halo: Combat Evolved
Halo 3: ODST
The avatar used to represent the AI Tycho from Marathon was added to the list of emblems under the same name as the AI. It is also the second emblem to be added to Halo with affiliation to Marathon.
A symbol is seen on a rock when the whole waterfall is visible, as well as inside the waterfall at the base.
Bungie avoided the use of the Marathon symbol in Halo: Reach, presumably due to property rights issues with Microsoft. The symbol has been removed from the emblem gallery, the difficulty icon shields, the hull of the Pillar of Autumn and replaced with the Seventh Column on Captain Keyes' ID patch. The symbol in the eye of the Forge Monitor has also been changed.
In the short story "Human Weakness" written by Karen Traviss, we see a new perspective on Cortana's interrogation and imprisonment by the Gravemind. This story makes the reference to the three stages of rampancy in the dialog from Halo 3 much more explicit and seemingly canonizes the concept of three progressive stages to rampancy within the Halo universe for the very first time.
Some Sangheili believe that "Demons" are actually corpses reanimated through artificial means to continue fighting as supersoldiers. This is reminiscent of the battleroids from the Marathon trilogy. Likewise, battleroids are brought back from the dead to serve as physically and technologically augmented supersoldiers. The player character is a Mjolnir Mark IV battleroid.