Okay, so I'm not a writer of fan-fiction (yet). I do however read it voraciously. Below are the main ships I follow.
Ships I LOVE!
Swan Queen: Emma and Regina
Xena: Xena and Gabrielle (the couple that started it all for me)
SVU: Olivia and Alex
Agent and the Waitress: Peggy and Angie
Rizzles: Jane and Maura
Facts of Life: Jo and Blair (yeah, I'm from the old school)
Skimmons: Skye and Jemma
Otalia: Olivia and Natalia
Calzona: Callie and Arizona
Faberry: Quinn and Rachel
JJ and Emily from Criminal Minds
SuperCorp: Kara and Lena