These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The original trilogy contains examples of:
Alternate Character Interpretation: Bernhard. Was he simply cruel to Durandal out of a power fantasy, or did he recognize the symptoms of Rampancy and attempt to stave it off as long as possible? Rubicon and Eternal follow each interpretation.
And Durandal is subject to this too, mainly in whatever he is an Anti-Hero or an Anti-Villain, or even an outright villain.
Big Lipped Alligator Moment: The earlier releases of the Aleph One version of Marathon started with the Pathways into DarknessShout-Out, which many considered to be this. Fortunately for them, there is a plugin that removes that segment, and then removed entirely in later builds. Funny, because Bungie considered adding something similar to Durandal and later Infinity, but both times it got scrapped.
Breather Level: Trips back to the UESC Marathon in the first game, expeditions into Thoth's domain in the latter two.
Demonic Spiders: The Pfhor troopers; they are the only enemies with near hitscan weapons (their assault rifles) that can do real damage on higher difficulties.
Compilers can fly, have a homing projectile that can shoot around cover, are quite durable, and can turn invisible. It doesn't help that they don't make any noise until they start firing at you, either.
There is a very simple secret to dealing with Compilers though: Punch them. Their recovery time takes longer than the duration between punches. With other enemies while punching you have to strafe to avoid enemy fire, but Compilers do not present this problem. Of course, if there's more than one Compiler at once that could prove more problematic.
Ear Worm: Swirls, a tranquil track that simply stands out in the soundtrack. Doesn't help that the first time you hear this, the game starts giving lengthy backstory text in the terminals (The History of Mars and the construction of Marathon in Couch Fishing), not to mention that it's the track for Colony Ship for Sale, Cheap which includes Durandal's more famous rants (Escape Will Make Me God) and That One Puzzle.
Splash (Marathon), by far the longest and most repetitive track in the game, which only makes the riff even more infectious.
It's more likely the Kudzu Plot. A ton of subplots were introduced or hinted at and dropped in the first game alone ( JJARRO WERE AT TAU CETI, anyone?), and some plot points seem to contradict each other, and not because of Infinity's Timey-Wimey Ball.
In some cases this is somewhat justified, as a lot of the information we have about certain aspects of the plot (most notably the Jjaro and the W'rkncacnter) comes entirely from mythological references by the S'pht. It makes sense that over thousands of years information would become somewhat Shrouded in Myth.
Germans Love David Hasselhoff: Not exactly super popular, but in Japan the relative popularity of Macintosh computers and the slow decline of home-based ones (FM-TOWNS, X68000, PC-98 and so on) during that time resulted in a fanbase of a respectable size, and that is despite the general unpopularity of the FPS genre there.
Goddamned Bats or Demonic Spiders (depending on the difficulty level) — Wasps, Compilers, Lookers, Pfhor Drones, Cyborgs with homing grenades, Ticks.
Hell Is That Noise: Various. The Jjaro station in Infinity occasionally lets a strained sounds of age and of general lack of maintenance...which sounds more like a barely awake Eldritch Abomination struggling against its prison.
Case in point: In the ending screen of Marathon 2 (which takes place many many years after the events of the game), he returns to the Sol system in a Jjaro dreadnought, playing cat-and-mouse with the human defenses near Pluto, and then suddenly warps into low Earth orbit. The reason for all of this? He wanted to say hi, and make sure people still remembered him.
Older Than They Think: These games helped pioneer the idea of story-driven first-person shooters before Half-Life (the game most often credited with this innovation) was even a gleam in anyone's eye. Marathon is also credited with being the first computer-based shooter to use the mouselook control scheme, and was at least one of the first shooters to feature secondary ammo and allied NPCs (the automated defense drones in the first game, then the BOBs in the sequels).
Paranoia Fuel: The Lookers in Colony Ship for Sale, Cheap. Lookers explode on you, similar to simulacrums, but they are very hard to punch without getting yourself hurt, they can fly, and some are camouflaged (they look like shadows). Still, not too much of a problem, since one bullet kills them. However, on Colony Ship for Sale, Cheap, they are in nearly every dark corner and every other corner in a hallway.
It's hard to emphasize how pants-crappingly scary this part of the level was.
The camo Compilers in G4 Sunbathing. They wouldn't be very bad if they didn't get together in groups of ten or more on Total Carnage.
Seinfeld Is Unfunny: This game introduced an incredible amount of things to the industry, being the FPS game that has a plot that is actually emphasized more than the action throughout the game, multiplayer modes other than deathmatch, vertical aiming, the ability for players to swim, AI-controlled allies… A few other games may have had these things, but not all at once. The list of things that this series introduced just goes on.
That One Level: G4 Sunbathing, Bob-BQ, Colony Ship For Sale, Cheap!, Habe Quiddam, If I Had A Rocket Launcher (M2), Begging For Mercy (M2), Acme Station (Infinity), Hang Brain (Infinity), You Think You're Big Time (Infinity).
If I Had a Rocket Launcher? Really? That was the most fun level in the entire series. In how many levels do you get to just wail away at an army of Pfhor troopers with an unlimited supply of shotgun ammo?
Who said levels can't be hard AND fun?
Sorry Don't Make It So is probably a much better example from M2 than If I Had a Rocket Launcher. However, by far the best example of this trope would have to be "Colony Ship for Sale, Cheap". This level's platform puzzle was so universally loathed by fans (you had to time a series of switch hits exactly right or you wouldn't be able to climb a series of stairs) that when the game was ported over to Aleph One they just left out the timing puzzle entirely and had the platforms automatically extend to the right locations (unfortunately, the original puzzle has since been reinstated in some versions of the game released since, much to various players' chagrin). It's also worth noting that the level's designer, Jason Jones, actually apologised for the level (most likely because of the puzzle) in the credits terminal for Marathon 2.
That One Puzzle: The movable platform puzzle on "Colony Ship". Nothing else in the series comes close.
In Rubicon, the enforcers. Dear god, I never knew a health bar could be drained so fast.
The Pfhor Chamberlains in the same scenario also qualify. They can't actually kill you, but they can strip your health bar down to the point where one hit from anything else will kill you, and they can do it in less than a second. Luckily there are only a few in the entire game.
Many of the A'Khr (and a few of the Pfhor) in Phoenix have infuriatingly fast firing speeds. These are the main reason the scenario is Nintendo Hard.
Breather Level: Some of the scenarios have these. In Pfh'Joueur, for example, the levels on the Nor'Haket tend to be less difficult than the surrounding missions, and in many cases have more to do with puzzle solving than they do with fighting off aliens.
The level "Roquefortress" in Phoenix is an excellent example: the level is extremely dark, if you take a wrong step you will die instantly, and enemies come from anywhere and everywhere and it is difficult to keep track of them. It does not help that many of the enemies in this scenario fly and don't make any noise until they fire at you, and can take away a whole bar of health in less than a second. Oh, and the level is set out in a completely non-linear manner so it's impossible to keep track of where the enemies have been released. Have fun! (Despite that, the level, as well as the whole scenario, is awesome, and one of the best examples of Scenery Porn created in the engine to date. The main creator has studied architecture extensively and it shows).
The swamps on the Pfhor planet in Rubicon have alien noises as random ambient sounds. There are also Lookers in the swamp (whose chatter is among the noises that happen as ambient sounds), and it's next to impossible to see them even if you have liquid transparency enabled due to the thickness of the sludge in the swamp. Needless to say, when wandering through the swamp, you're pretty much constantly afraid that you're going to walk over a Looker and die.
That One Level: Secret levels tend to be infuriatingly difficult, although there are exceptions (the last secret on Tempus Irae is mostly an excuse for porn).