This is an addendum to the FAQs, added by link so that people who don't want spoilers have a lowered risk of getting them.
It was suggested that I put together a quick list of the pairings for Game of Dreams. I don't really like doing that, because dammit it spoils the story, but people keep asking, so yeah, here you go... a not-very-quick-at-all list of pairings involving canon characters in YnY. I may edit this as time goes by.
Be warned, I like convoluted pairing bunches. (And be reminded, GDG, the person who wrote most of this part of the plot, is bisexual, so if you're bothered by some of these pairings I'm sorry but I'm not changing it. Also I get kinda touchy about gay bashing, so watch your step.)
Red highlights indicate that offspring resulted from the pairing, more specifically, offspring characters who will definitely play a role in the post Game of Dreams comic. (Some of them I haven't actually decided yet.)
Yugi/Téa- Yukai, the titular character of Yukai no Yugi, is a result of this. So is his 'orrible ikkle sister, Anna.
Yugi/Rebecca- Rather one-sided.
Bakura/Téa- Short lived.
Marik/Téa- Also rather short lived, and mildly convoluted.
Atem/Téa- Totally one-sided, because he's dead.
Bakura/Somebody Else- Well, he DOES end up with a daughter, and it kinda takes two to do that.
Bakura/Atem- Heavy undertones.
Marik/Somebody Téa Introduced Him To- Marik has two kids from this, although one is adopted.
Pegasus/Ishizu- In turns handled with maturity and childish enthusiasm.
Pegasus/Cecelia- Well duh. Not heavily touched on for obvious reasons.
Seto/Serenity- Kira, whom Yukai is madly in love with, is a result of this.
Joey/Seto- Heavy undertones that Kaiba would never, ever admit to anyone, ever. Also perhaps a touch one-sided. (That does not mean he isn't in love with Serenity, mind you.) (Also you could ignore the undertones if you wanted, but why would you want to?)
Joey/Mai- They have five kids in YnY proper, one of whom, Ken, is in Yukai's grade.
Alister/Seto- Lightly touched on, although whether it's one-sided or not is... vague.
Mokuba/Rebecca- Mostly in the form of leering.
Leon/Rebecca- Not so much in the form of leering.
Mokuba/A Chick From His Class- "Bad Mokuba! Stop staring at the skirts!!"
Zigfried/Somebody- I'm not spoiling how they meet, sorry.
Tristan/Serenity- One sided and short-lived within the story itself.
Duke/Serenity- Smashed to pieces.
Tristan/You'll Never Guess Who- And they have a kid together, too.
Duke/Someone I Borrowed- Amber, with whom he has a daughter, Jade. (I know the Japanese anime hints that he might be gay. I don't care; remember what I said before the list.)
Mako Tsunami/That Lady From The Aquarium Show- They have triplets. =3 Pretty much background fluff.
Yami Bakura/Mildly To Very Abusive Persons- I was looking through the backstory and the future plot notes and was amazed at how many different people physically or psychically abuse him in this. Including a tall but very skinny woman and her twin brother. O_O
Yami Marik/You Won't Drag It Out Of Me Until It Happens- Yami Marik appears in YnY?! Wtf? (But not in Game of Dreams, so you can relax.)
Okay, so some of you might have gotten through this and are now going "Oh, Ra, she's screwing with us again." No. This is the most candid I am ever going to be about the pairings. Like I've said many times, I don't like telling pairings because I find it spoils stuff for a lot of people. But I also appreciate that some people prefer the spoilers, much as I hate doing it.
Keep in mind that Game of Dreams is intended to set things up for a next generational fancomic, so certain of these pairings were chosen as much for the offspring they potentially produce as for the pairing itself. Kira and the Wheeler kids are a prime example of this: if I had paired differently there, Kaiba and Joey's kids wouldn't be cousins, which is hilarious enough that I'd have done it even if I didn't already adore silentshipping. The mother of Bakura's child was designed specifically so that his daughter could logically look like a female version of his Series 0 color scheme. Yukai, in his own perverse way, takes very heavily in personality after Téa, and not as much after Yugi.
Some of the pairings will not last very long within the story. I've always thought it rather odd how many people want all the pairings in a story to be sustained the whole way through; I find it boring myself. Relationships change. Sometimes a crush stays a crush, and sometimes you break your heart instead of going after someone because you know they simply can't want the same thing you do. Sometimes people fall in love with more than one person at once. And sometimes a combination of those things happens. I've never really been much for traditional fictional romances, certainly I'm no good at writing that kind of romance. Convoluted polygons are what make me happy. (Which is kind of stupid, because they're sure as hell not much fun to actually participate in, but there you go.)
Most of all, once we get out of Game of Dreams and into YnY proper, there'll be a whole new kettle of fish to deal with. This really isn't intended to be the kind of story you read for the pairings. I've said it before; if there's a pairing you'd like to see me play with, hit me up about it and I might post something to my FF.Net or my main DeviantArt account. (Might. I don't take requests anymore, only friendly suggestions and niggling thoughts that won't go away. Requests just seem to get me in trouble.)
You can find a very long but not totally complete list of shipnames at the WikiFic Wikia.
Yes, I totally consider a one-sided crush in a fic to count as a "pairing," even though nothing physical happens.