Synopsis: it's a monologue of Samus' thoughts during the last section of Metroid Prime Three. it's an interesting look into Samus' personality and the way she looks at the world, painting her as finding the life that she leads difficult to say the least.
Synopsis: (from the author's profile page) "Twenty years after the Aether incident, Angseth, the sole survivor of that horrible event, finds herself as a Confederation Battle Cruiser Captain on the edge of retirement. Until strange events once again cause her path to entwine with Samus Aran."
Comments: An extremely well-written science fiction story told with a minor "what if?" within the framework of the Metroid universe. Players of Metroid Prime 2 may recognize Angseth as the name of one of the dead Federation troopers encountered in the game. This story is the result of the author thinking, "What if she'd survived?" It works. Quite well. Primarily an OC fic, Samus Aran (the games' protagonist) makes very few appearances. However, the story maintains the feel of the Metroid universe. Through the course of the story, the main character gets into scrapes with just about every hostile entity you might expect, while continually (and mostly unintentionally) getting more powerful all the while.
Status: As yet, the story is sitting unfinished at 27 chapters, and is slipping dangerously close to Dead Fic territory, though it is still alive and its condition seems to be improving (last updated 6/28/09, several months since the last chapter).
Update: Two chapters have been added since then, with the most recent one being added on 5/4/10.
Not available on FF.net as of time of writing (2/20/11). First four chapters available here.
Update: As of Jan. 7, 2013, it's back. "Reposting/rebooting my fics. Took the time out to work out (hopefully) all of the grammatical and layout kinks. I will post chapters as I finish them." 
Updated original link with new URL. (I'm the original rec'er with a new username.)
Synopsis: "Samus runs into a Federation technician in a bar. They chat about technology in the Metroid universe. An exploration of the power suit's underlying technologies."
Comments: While less of a traditional fanfiction and more of a fan's personal theory, it's an interesting story about the Power Suit, and it's totally believable. Right down to Samus getting multiple drinks from some guy in a bar.
Synopsis: From Fanfiction.net: "Crippled and half-dead from a failed mission, Samus Aran now fights against an even deadlier lifeform than the Metroids, her own body now fused with the extinct monsters. Novelization."
Synopsis: From Fanfiction.net: "Samus. Metroid. Hatchling. A piece of planet SR 388 has stabilized its orbit around a small star and Samus is inclined to investigate if the X still exist. She goes there despite protests from the Federation and the malfunctioning of her power suit."
Comments: Expands the canon events in the series, primarily Fusion, with flashbacks to events from other games and the manga for Samus' childhood. Fleshes out Samus' personality and feelings, portraying her as a warrior, a motherly figure, and a lonely girl. Features interesting character interactions, issues with Samus' Metroid DNA, and an original post-Fusion adventure. Unfortunately, Hatchling seems to have entered Dead Fic territory, with the last update in February 2009.
Synopsis: From Metroidgalaxy: The Huntress Series of stories I have written are based around Samus Aran, shortly after she destroyed Planet Zebes. At the time I wrote these, I hadn't played Metroid Fusion, and so I had no idea what took place in that game and therefore could not write what took place afterwards in my Fan Fictions. So I simply excluded that game from this series, my apologies if Fusion is your favorite game and you would like to have it included, but many have said that these stories aren't too bad. In my personal opinion some parts could stand to be redone, but I am happy overall with the final result of them.
Comments: Sadly the site that hosted the series is not up anymore, however the internet archives have made the site as well as all 8 of the stories available. The Huntress Series expands on what Samus is like outside of being a bounty hunter, the struggles she has gone through in her life, and how she deals with them now. It features many twists and turns that make for a very engaging story that drags you in and never lets you go. Interestingly, much of the series fits into the current canon quite well.
Synopsis: From the author's description: Oneshot: As Aether's battle has taken its toll on the planet, the life living on it struggles to stay alive. The Luminoth aren't the only ones sleeping in the Great Temple...
Comments: A neat little one-shot told from what I think is a very unlikely perspective, that of a flock of sandbats in the Great Temple on Aether. Short cameo by Samus near the end sort of sticks out, but otherwise a very good effort here. Re-caps the status of Aether at the beginning of Metroid Prime 2 pretty well. It might almost be too short, but in my opinion it tells what it has to very well and doesn't overstay its welcome.
Synopsis: from the author's page: 'Post-Fusion. When the Federation condemns Adam for his role in the BSL Incident, Samus enlists the help of a young scientist to save him. As sinister forces array against them, they must race against time to uncover a conspiracy of galactic proportions.'
Comments: This was one of my first fanfics I had ever read, and if it hadn't been for it, I probably would have quit. The story is LONG but totally worth it. The mystery surrounding the conspiracy is very dense and intelligent, and you see the detective work of Samus and the scientist, CJ. Speaking of which, their relationship is incredibly believable, and you do see the relationship grow. The last scene of Chapter 12 is one of the most heart-stopping moments I have ever read. Plus, there are author notes that explain the science behind each chapter and includes musical selections for the chapters.
Synopsis: From the authors' description: "Even legends have to start somewhere. An exploration of Samus Aran's rise from obscurity to greatness through a collection of independent, interconnected stories."
Comments: An oldie but goodie (to quote the authors, "Five years ago this thing started. Christ."), and very much in the style of Cowboy Bebop with a subtle hint of Metroid. SYNM is a series of linked oneshots that look at the rather hardscrabble beginning of Samus' career as a bounty hunter, long before she got involved with the Federation. Notable for excellent writing and plotting, as well as a truly amazing degree of Shown Their Work; everything from the Federation's economy to the legal underpinnings of bounty hunting in the Metroid universe gets addressed at some point.
Status: In Progress... but looks like it's entering Dead Fic territory, what with the last update being in Feb. 2010.
After over a year and a half of deadness, it has updated in Sept. 2011.
Synopsis: Post-Fusion. Samus is hired by the Federation to track down a renegade squad of GF Marines who have stolen a deadly chemical weapon and plan to sell it on the black market.
Comments: Definitely an action-packed read. The pacing is excellent, and the plot comes together beautifully while having enough enemies strong enough to take on a fully-powered Samus without Nerfing her. And despite the sci-fi setting, the basic plot is a dead ringer for today's troubled times with the threat of a WMD on the open market. If ever a Metroid movie is made, this is the style it should follow.
Synopsis: from the author's page: 'After the events of Metroid Fusion, supposedly, the galaxy is at peace. However, with a hidden conspiracy being developed along with a master plan the Space Pirates will administer, it is not even close.'
Comments: This fanfic, starting mere days after Metroid Fusion's ending, begins with the Federation declaring a golden age is nigh. Then a lot of character (re)introduction ensues, followed by Samus crashlanding on a nearby planet in an attempt to escape the Federation. Shortly after... Samus joins the Space Pirates. In order to combat the corrupt Galactic Federation. This happens in countless Metroid fics, but this fic executes it particularly well, and the allegiance is actually somewhat believable just because of the way the author explains it. There are very few OCs (not counting creatures), with many old faces at least poking their head in for a bit. In particular, all of the hunters from Prime Hunters are mentioned and some are characterized. The whole fic seems to be inspired by all Metroid games in fact, because all of them get an homage in their own way. If there's anything negative to say, it's that the description at times is rather lacking, but the dialogue, plot, and characterizations are particularly fantastic. Definitely worth a read.
Status: In progress... and may be a Dead Fic. It's currently at 17 chapters and approximately 70-75 thousand words. The last chapter was posted fairly recently, but it's pretty lacking in overall quality — the author, however, expresses interest in both rewriting chapter 17 and finishing the story without rushing it.
Synopsis: A very good Alternate Universe fic following not Samus, but a Space Pirate (known later as 'Dr. B') that becomes self-aware due to Phazon mutation. This space pirate explores his new sentience, builds his identity, and devotes his life to studying the elusive idea called 'I' that gives sentient beings their true power. At times, he tags along with Samus. Other times, he follows the events of the Metroid canon that Samus was not there to witness...
Comments: This fic is written by Seldavia, who has authored three (count em, THREE) stories listed on the FanficRecs page for The Legend of Zelda. She has not lost her touch, and is currently even writing a sequel, known as The Unsinkable Dr. B. An interesting thing of note is that the thought process and identity discovery of the main character of the Dr. B series mirrors many issues and traits associated with the autism spectrum. Not only that, but the characterization of Samus both manages to be professional, empowered, emotional, yet very sensible— overall a merit to the Metroid Fandom.
Synopsis: Because of Samus's very unique genetic makeup, a bio company puts out a bounty on her egg cells to make the perfect warrior.
Comments: Only in the prologue now, but a very interesting concept that makes use of some Fridge Logic from the Metroid-verse, such as Samus actually being much lighter than she looks because of her bird-like Chozo DNA. Warning, very explicit.