To make a long story short: I used to share links to old Marathon or early-Halo stuff I found on me blog, but then tumblr began squashing posts with links to sites not on an undisclosed, very small whitelist, in the effort of dealing with pornbots (which didn't work). Then they began squashing posts with any links, even internal ones. (It still didn't work.) Then the site situation got so bad that I've finally mostly-left, but I digress.
Many of the following were found via Wayback Machine. This post will probably be updated in the future, if I or other folks find more noteworthy links--old Core/rampancy.net threads that were actually archived, fan scenario-related stuff, etc.
Duardo.net. Most links lead nowhere, but the Bungie.net image archive and Disembodied Soul simulator work.
Aleph One circa 2005. A good deal of the fanart and icons are still available.
Fileball. Something I didn't know before stumbling across it was that it hosted non-Marathon content.
Cortana.org. Technically this would go under "Halo", but the only names listed near the top are Marathon-related (plus a mysterious "Balmung", that I made an OC out of as a way of dealing with the link not actually leading anywhere).
(6/18/19 EDIT: It's likely that "Balmung" was a Myth reference I didn't catch, though this raises the question of why a non-sentient sword is listed among actual characters. Did they still try to make Balmung an AI, or was this a "Marathon and Halo are totally in the same universe as Myth" thing?..)
Tru7th.org and an archive of the site's contents. Primarily a humour site with some early-Halo stuff.
Hiroking's site. Contains some fics (all in Japanese, obviously).
Lem's Comic Room, which has some Marathon stuff. (JP)
"Jade Incursion". One of many unfinished Marathon scenarios; screencaps are busted, but text stuff is archived.
Screencaps for "Cerberus".
The Rubicon site, circa 2002. Mostly here for its development history section. (Note: ages ago I came across a different Rubicon spoiler guide, and the only part of the url I have remember is "inio". Maybe one of these days I'll find it again...)
EARLY HALO STUFF
Pax Nimbus, Brotherhood of the Halo. Basically a webring that's old enough that Marathon and Halo are put in the same category.
Bungie's own list of Halo and Marathon fansites. Yes, both series.
"Welcome to Halo", by Ferrex (of The Core, later rampancy.net). Made a lot of historically-interesting assumptions about Halo, Marathon, and how the former's fanbase would be a sort of hybrid of Marathon's and Myth's.
Battleground Halo, a site whose team members included folks from the Tribes and C&C communities.
An official Gearbox-run modding site, hosted on Cortana.org (the same one as above?).
Long Letters-based thread. (6/30/99 11:01 a.m.)
No, player, YOU are Cortana! (7/6/99 5:31 p.m.)
Single post about the Letters possibly detailing events in chronological order, with the final letter assumed to be the endgame. (7/26/99 8:05 a.m.)
Lengthy analysis beginning with a question of Cortana's identity. (7/27/99 4:11 p.m.)
Cortana was the top Myth 2 player. (8/18/99 4:11 a.m.)
Another "who is Cortana?" I distinctly remember this thread providing the inspiration for my OC, Hero. (10/4/99 12:51 a.m.)
"Why did Cortana lie to Foehammer?" (1/28/03 11:24 p.m.)
These three fics by Jägermeister, written in terminal format.
"Construct" by MacGuyver, about a guy whose memory Cortana tampered with.
"The Law of Sin and Death" by David "Paladin" Huang. A fairly long fic detailing the start of the not-yet-released game as imagined by Paladin.
"The Righteous and the Wicked" by CUTS, involving the Jjaro's relationship (such that it is) with other species.
"Before the Storm" by Chris Cox. Contains pre-H:CE assumptions of the nature of Master Chief, with bonus ‘if SolCore is the main human-based force now, what happened to the UESC?’
"Of Gods and Heroes", "Untitled", and "Untitled 2", plus "Bracelet of Gods", "The Mantled Wings of Angels", and "The Desperation of Dreams". All six are by Apeman; the first three deal very heavily with early Marathon/Halo speculation, while the latter three were written closer to H:CE's release but still feel distinctly Marathon-flavoured. I don't want to give away what happens in the first set of fics, so I recommend checking them out yourself.
"Durandal" by Craig Hardgrove. Some Infinity-esque text.