The saga that inspired the X-COM page on TV Tropes... and the exhaustive coverage that drove Guava and Jade nuts. Note that these are listed in order by internal chronology; Guava actually played Apocalypse and Interceptor first, then Jade did Aftermath, then they started collaborating.
Ssfsx17: This is an absolutely epic saga detailing the life and times of an X-COM soldier by the name of Otto Zander, with some interesting custom missions made specifically for the LP series.
It would seem that Otto Zander is now an "official" unlockable character in the new XCOM remake by Firaxis. A great little piece of ascended fanon.
Speedball: It's a fantastic comedy of errors where everyone keeps dying...and yet also gets serious when it becomes time to, like all great fiction. Seriously, check it out.
From the website that brought you The Salvation War and the author that brought us Tiberium Wars, Forward, Renegade, and Harbinger comes another tale of indiscriminate use of firepower against a threat humanity has to mentally dissect in order to conquer. Currently Dead Fic, due to the author suffering a Heroic BSOD following a traumatizing defeat while assaulting a Muton base.
Pilfering equal parts from Red vs. Blue and Warhammer 40,000 to create a tongue-in-cheek hyper-Spartan mentality, these two somehow manage to survive X-COM's insane Red Shirt turnaround and turn that luck into ensemble comedy. Currently Dead Fic since Alex Knight's computer crashed halfway into TFTD.
Stories focused on the family and the friendly relationships of the cast. Plot-focused stories or light day-in-the-life stories. Pretty much anything that isn't focused on romance.X-COM Saga by Russ Brown.
Synopsis: This is EPIC, in the truest sense of the world. It covers the entire First Alien War (UFO Defense) from X-COM's beginning to the final battle at Cydonia (1998-2003). 36 chapters of brutal combat, political intrigue and conspiracy. André has managed to pack a lot into this story, bringing the game to life and giving us characters that you care about.
Comments: Worth noting that the writer's first language is not English, so this can make some parts difficult to read. Nonetheless, extremely well-done and properly thought-out, adding in political and conspiracy angles that the original game couldn't offer.
They Killed Fritz: It's worth noting that, although the original novel is complete, as is the intermediate short story 'Eulogy', the full sequel 'Abyssal' is currently Dead Fic, and will likely remain that way permanently - the most recent update, the eighth chapter, was posted in 2005. As such, it is likely that the third planned novel, 'Nemesis', will never even be begun.
Synopsis: SG-1/X-COM Crossover — As humanity fights two alien threats its defenders join forces to turn the tide
Comments: "suprisingly good" doesn't even scratch the surface. This fic is made of concentrated awesomeness mixed with a healthy dose of HSQ.'
Night: Feel-good asskickings abound. In other words...NOTHING LIKE X-COM.
Mandemo disagrees. It's exactly X-COM. It's just Jaffa suck compared to sectoids, etherial or crysalids... Still, X-COM spends most of its time trying to figure alien tech out, as several situations at are very grim (Alien fighters fromInterceptor against UFO Defense equipment? Oh Crap). Still awesome!
Synopsis: 'SG-1/X-COM fusion fic - it's about XCOM: EU Earth running their own Stargate program staffed by a bunch of XCOM style familiar faces from Stargate - both Carter and Jackson are psionic, and so are a few Goa'uld. The author has hinted that the slightly diffrent Stargate galaxy the Earth of the story finds themselves in is a result of some sort of conflict/relations between the Goa'uld and the Etherals... and that we should all be scared witless when the already psychic bad guys of Stargate show up. It's written from Jack's perspective in first person and is actually quite funny at times - even if the main draw is the kickass action on a scale never dreamed of by SG-1 or XCOM.
Synopsis: 140 years have passed since the Ethereal War, leaving sociocultural scars on humanity's psyche. When a scientific team is attacked by unknown aliens while investigating a mysterious megastructure, the lingering paranoia is justified all over again. Enemy Unknown continuity, crossover with Mass Effect.
Synopsis: MLP:FIM/X-COM Crossover — Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?
Comments: Completed, with 2 completed Side-story sequels, and and a 3rd sequel currently updating.