I have a great deal of love for Bobby/John/Marie in various combinations thereof, and am an easy sell when it comes to Xavier/Magneto. That said, I'll read most pairings and like all the characters.
Jump around : Stand Alones / Series
The Last of the Jedi by Artaxastra
Cool, interesting Jean backstory which grounds things in real life events and gives wonderful texture to the characterisation and relationships.
When You Had the Chance by J.J.
Desperate, bittersweet, foreboding and painful Charles/Erik. Every word means something and the end left me breathless.
Shattered, Rebuilding by Emerald Blue
Perfectly characterised Charles/Erik.
His Mother's Eyes by Artaxastra
Wonderful story about Kurt and Mystique.
Barbecue by Twinkledru J
I like the main idea behind this story. It's totally cool, and I love the characterisation (of Xavier especially).
Cold Cold Heart bybackfromspace
Johnny writes Marie a letter and it's wonderfully bitter.
Burying the Dead by Victoria P
This is a dark and amusing look at Logan and Rogue some time after the first movie. Very cool.
Freeze Out by zahra
Sexy Bobby/John UST, with a really cool look at the way Bobby reacts to Johnny fidgeting with the lighter.
Maybe by backfromspace
This is short, with wonderful description and makes it's point nicely. Cute.
Passion Has Red Lips by Victoria P
I'm not particularly fond of the Logan/Rogue pairing, but this is cute and makes it work.
Skin And Bones (Self-Delusion Mix) by Jengrrrl
Oh, this freaks me out. It's ostensibly Logan/Rogue, but there's this whole thing with Mystique as well. It's dark and twisty and pretty darn cool.
Stray by Victoria P
This is just utterly cute, plus I like the interaction between Logan and Rogue in this.
Sunrise/Sunset by Pablo
I love this pairing. It's more sexy Bobby/John, with really cute muddled Bobby moments and lots of nice rolling about in bed.
There Goes the Fear by zahra
This is wonderful Bobby/John full of awkward first times and mistakes. I really like this, especially the end which hurts.
Unbound by FayJay
I really like this look into Wolverine's mind and dreams after the first movie. There's a nice use of detail, and I can really believe the characterisation.
Between Oranges and Apples by Mary 
I love this story. It looks through Marie's eyes at her childhood at various points and the B/M/J love triangle, using lots of lovely little details about smells and fairytales and other things. The characterisation is great, and I like the way some things are hinted at in this story. I love the mood of this story. This is really good.
Sometimes Mystique.. by Meli
This is a short and sharp look at Johnny and Mystique, after the movie.
Every Second Wednesday by Jenn
This is an interesting look at the people in Marie's mind and the way that might shape her interactions with Xavier.
Guessing Games by Andraste
Mystique contemplating Charles and Erik. This is very interesting. I find her perspective on things very intriguing in this story.
In Dreams by Elizabeth
This is an interesting look at one of the ways Rogue might have dealt with having Magneto in her head. I particularly like the description of the prison and the way Rogue sees Magneto. Very nice.
Event by Te
Cute story about Bobby meeting Hank McCoy.
Flaw by Te
Strange, but interesting piece about Erik.
An Ephemeral Composition by Te
It's told in a somewhat chaotic manner, but it's still a cool Erik piece.
Little Scenes From A Greater War by Spyke Raven
Suitably screwed-up piece about Mystique and Magneto. It's way cool.
Mixed Feelings by Andraste
Ooh! I really like this. Marie deals with Erik in her head and talks to Xavier about it, and it's much better than the average story with that plot.
Universal Truths by Elizabeth
Xavier thinking back on Erik. Very nice. The characterisation is really good and I like the way this is written.
Aesthetics by Zahra
A nice little look at Bobby's attraction to John.
Of Cakes and Longing by The Net Slayerette
It's Rogue/Jean and it's actually good. Colour me shocked.
Twist by dafnap
I like this. John being a prat and Mystique being cruel. It's strangely satisfying.
Goodbye Bobby by Minna
John's thoughts towards the end of the movie. Short and to the point. Nice.
Le Petit Mort by Sonatine
Short, sexy Bobby/Marie piece. Yummy.
Patience is a Virtue by xfan
Mystique pondering Logan and his rejection. Short, but nicely put together.
Pleasure by Te
This is a fabulous Mystique story, with a lovely perspective on her relationship with the Brotherhood, and Erik especially. I really like this one.
Unheimlich by Gemma
Charles and Erik and mind games. This is pretty cool.
A Good and Righteous Man by Dyce
Vignette from Senator Kelly's POV. It has power.
Third Wheel by Adrienne
This is totally cute and funny, and, you know, I dig this threesome. The characterisation really works for me, and I really dig the tricycle thing, even if it is kind of demented.
Still-Waking Sleep by Mary
Wonderful St. John POV of the relationship with Rogue and Bobby, after the end of the movie. I really buy this characterisation.
Bari v'Shalem by Chloe
Hot B/M/J threesome. Yummy.
Last Season By Akazukin Elle
It's a wonderful little look at Bobby contemplating his relationships with Rogue, Bobby and the universe, with lots of little details I just adored.
Ten Thousand Candles By Andraste
This story is just fantastic. It looks at Xavier after the movie, and that terrible thing the end of the movie glossed over. It's a great look into the character and has such wonderful details. There are some really great lines in this story. I love it.
A Little Is Enough By Ascian
Oh, this story about Kurt is just adorable. Also, nice look at the grieving after losing Jean.
The One Left Behind By Bek
A look into Scott's pain after, that just feels right.
Chele Kodesh By Chloe
This is kind of strange, but totally cool. Johnny's life after he defects to the other side, and I like the way it's depicted.
Original Sin By Elaine
Short but sexy Kurt/Ororo.
Always Hungry By Jane St Clair
Fantabulous Bobby/John, wherein John seems so perfectly like a teenager.
Agonia By Minisinoo
I really like the way Scott's grief is expressed in this, and I like the Kurt characterisation. It's very nice.
And Life Goes On By Nix
A cute Kurt story.
Sanctuary By Nix
A marvellous Kurt story, set after the attempt on the president's life. I really like this look into his mental state, after.
Acquiesce By Pablo
This is sexy Bobby/John and very nice. I dig the Bobby characterisation in this.
Devil's in the Details By Serial Karma
I was hoping someone would write something like this. Sexy little story about Mystique and Johnny, and the way he feels about those he's left behind.
Sidelines By Shelly
I love this. Johnny is perfectly frustrated and angry in this, and the slashiness is cool. Some nice lines and good use of POV.
The Third Day By Tami
Storm cries after losing Jean, Kurt tries to comfort her, and it's just really sweet and sad. Peppered with lovely details and characterisation I can get behind. I really like this one.
To Drown in a Sea of Tears By Winged Elf
I really like the idea of Kurt watching everyone's grief and being concerned for Bobby. This is nice.
Dreaming by Amber
Poor Bobby missing his Johnny. This story makes me want to pat him.
Before Rogue by Duckie
Short and to the point B/M/J goodness.
Just like old times by Nightbird
Mystique is just full of possibilities. I like the way Johnny pretends in this story.
Night one by Pearl O
Johnny misses his friends, and there's just a hint of things unsaid in the background. I really like the brief bit of Magneto in this. Very cool.
3 Stops Automatically by Jori
Sexy B/M/J goodness, heavy on the slashiness. I like.
On Love and Lust at Mutant High by Jenn
This is just so cool. It's a gzillion parts of St. John/Bobby goodness. I am so in love with this series.