Tea x Atem/Yami Yugi (I do not differentiate between Yami and Atem as people; they are the same soul. And yes, this pairing is pretty canon but I love it and I love the confusion/realizaiton/complication from realizing she is in love with someone who shares a body with her best friend.)
Joey x Mai---LOVE it. I wish they had kissed in the anime.
Tristan x Serenity--I used to really love this one, but I can go for other Serenity pairings as well. Serenity/Seto and Serenity/Valon are both really interesting.
Seto x Kisara and Priest Seto x Kisara (I am thinking about writing a fanfic about Kisara being reborn into Seto's era, but not having her die)
Priestess Isis x Priest Karim--I love this one, but everyone pairs Isis with Seto or Mahad. someone tell me some good Isis/Karim fanfics!
Mokuba x Rebecca -- so cute! I used to really like Yugi x Rebecca, but now I'm not so sure about that one.
Tea x Marik--in my head canon, Tea is Yami's soul mate, but the idea of Tea and Marik is really, really interesting. Especially since it's like good girl/evil guy, and since he literally lives in her head for a while during Battle City and since he forcefully possessed her when they first met. Plus I've read a couple really good fics with them.
Yami Bakura x Marik--the only yaoi pairing that I like. In general I don't care for slash at all but this one is kind of intriguing.
Duke x Vivian--I kind of like Duke/Serenity, but I saw a fan art pic of Duke and Vivian and that got me to thinking about it and the more I think about this one the more I like it.