Gaila, Uhura's Orion roommate, is a fan favorite despite having only a couple of minutes onscreen. In fanfiction and fanart, she's paired with Uhura, Scotty, Sulu, Kirk, and even Spock - especially Spock Prime.
DeviantArt is filled with fanfiction and fanart pairing Heath Ledger's Joker with Cillian Murphy's Scarecrow, Gary Oldman's Gordon, Christian Bale's Batman, Ramirez, as of yet unintroduced Harley and the Riddler, random Mary Sues, Aaron Eckhart's Two-Face, Maggie Gyllenhaaland Katie Holmes's Rachel, and anything in the Nolanverse that moves. I haven't found a Joker/Alfred one yet, but I wouldn't be shocked. And that's nothing compared to what they do to poor Scarecrow...
And that's just the in-universe examples. Outside of that, he's paired with everyone, including Rorschach from Watchmen.
Probably a combination of being portrayed by Tom Hiddleston and how sad his Start of Darkness is, but Loki has become this from Thor. A brief trip through Fanfiction Dot Net will turn up stories shipping him with Thor; Tony; Steve; Clint; Natasha; Coulson; The Hulk; Sif; Jane; Darcy; Angrboda; Sigyn; Fandral; Baldur; Tyr; Pepper; Amora; Lorelei and even Nick Fury, along with many, many more.
He's even shipped by some with his own actor. That's what happens when you say your character needs a hug...
Another one is Steve Rogers, partly because he's played by Chris Evans, and partly because he's either viewed with a lot of "uke" traits (being younger, old-fashioned, and relatively innocent compared to his fellow heroes), or a paragon of manhood who can be strong, protective, and sensitive to other people's imminent emotional breakdowns. His portrayal depends on whoever he's being matched up with (i.e., Peggy Carter, Tony Stark, Bucky Barnes, Loki, Howard Stark, Phil Coulson, etc).
Darcy, with a healthy side order of Ships That Pass in the Night. She's frequently shipped with Loki, Hawkeye, Steve Rogers, Bruce Banner, Bucky Barnes, JARVIS, and Coulson, only one of whom she's even met. On the slash side, she and Natasha are getting shipped together increasingly more often. The Archiveofourown fic site even has a tag labeled 'ship Darcy with all the things' that currently brings up 92 stories. Next to Loki, she might be the biggest bicycle in the fandom. 'Darcy is the fandom bicycle and I love it' is nearing 100 fics as well.
Black Widow, stemming from having a lot of this in-universe. Her flirty personality and the fact that she's the most prominent superheroine helps, but she's had some degree of Ship Tease with a large amount of the male cast. In addition to Fan Preferred Couples like Clint and Steve, other popular pairings include the rest of the Avengers, Loki, Bucky, Sam, Pepper, Maria Hill, and of course Darcy. (And after the sequel, Bruce Banner).