A MegaCollection Kit

Please let me know of anything else I could add in the comments at the bottom.

Bungie's cerebral Mac adventure, now open-source

The Original Trilogy

Marathon, Marathon 2: Durandal, Marathon Infinity: Blood Tides of Lh'owon

Source Port

Aleph One is pretty much the only one. Site even comes with preconfigured downloads for each game, so no setup is required.

There's even iOS ports on the App Store. Alternatively, the Marathon Trilogy Box Set's Definitive Map Collection can be used if you want to use a Mac emulator, and contains over a thousand maps and add-ons.

Multiplayer

Lhowon.org is the primary game server (and host of the Aleph One site). Most online matches are played with Infinity as far as I know.

Mods

The Aleph One site has links to the following scenarios on their scenarios page.Marathon: EVIL is the first conversion for Infinity, and is considered to be one of the finest (and scariest). Tempus Irae takes you back in time to Renaissance Italy. Marathon RED is survival horror-esque, and is known as one of the hardest scenarios. Eternal is one of the largest. Marathon: Rubicon X is a fan continuation of the original trilogy. Marathon: Phoenix is action-packed. Istoria is an RPG with multiple classes and spells, and the ability to talk to the dead with a text parser. Mararthon: Yuge is a community collaboration.

In terms of mods not listed, Excalibur: Morgana's Revenge is a time travel adventure with no connection to Marathon's plot. Pfh'Joueur is beautiful and short. Marathon Apotheosis is atmospheric and often terrifying.

If you want the classic HUD, use Marathon Classic HUD.

Find More

Simplici7y is the community's primary file sharing site. Also try Fileball or The Archives. The Big House is another host of scenarios.

Make

Weland is the primary map editor. From the Pfhorums, RyokoTK's mapmaking guide and $lave's Recommended Editors.

Other Sites

Bungie's Official Marathon Site, The Trilogy Release, The Official Marathon Vidmaster Page, The Pfhorums, Marathon's Story Forum, Marathon's Story Reference and Analysis, Aleph One Github Wiki, TV Tropes page (lot of useful links)

Youtube: Marathon Vidmaster Challenge & Occasional Metal

Background taken from here.

Suggest more in the comments!