In the omake where all of the cast are high school students, Lucy talks about how much she adores her cute and nice classmate Mirajane. As if that wasn't Les Yay enough, Elfman soon tells her: "If any guy wants to date my sister, he has to be stronger than me!". Lucy's reply is: "Well, I'm not actually a guy, so..." Yeah, Lucy is much more busy about denying the accusation that she is a guy than the accusation that she has a crush on Mira. Make of that what you want.
In the Fairy Hills OVA, when the girls are discussing who likes who, Laki says she thinks Lucy likes Mirajane.
In the "Freaky Friday" Flip episode, Levy volunteers to help get everybody back to normal. Lucy thanks her, and Levy answers, "Anything for my girl."
Lucy x Juvia: Tower of Heaven arc. Lucy and Juvia were able to use the powerful spell Unison Raid, which requires the partner's hearts to be in perfect synch, on their first try. Jellal noted that some couples could work together for years and never be able to do it. After the spell, they fall asleep in each others arms.
The fifth OVA has them both going down the love slide together, in a rather compromising position. Bear in mind that two other pairs going down together are Gajeel and Levy, Erza and Jellal, and finally Elfman and Evergreen.
Lucy x Aquarius: In S&M, Lucy would be the slave.
Lucy x Virgo: In S&M, Lucy would be the mistress. And Virgo changes Lucy's clothes for her, once while Lucy was asleep.
Corollary to the point above: It's also worth elaborating that said spirit assumes a form and personality that reflects what its current summoner desires. Its last owner had weird tastes so it was an aggressive gorilla like Gonk. For Lucy it's a submissive, masochistic and highly attractive Emotionless Girl.
Chelia x Wendy: Even though they've had chemistry only for a little while, it's blatantly clear that their little friendship moment is foreshadowing to the fact that Hiro is catering towards the lolicon audience. Especially as of the recent chapter, Chapter 298, where they run off together, and after Natsu destroys the building they're in, Wendy lands suspiciously on top of Chelia.
Freed x Laxus: It is a fact that Freed looks at 3D magazines with naked male Blue Pegasus members. Bearing that in mind, Freed has a giant Laxus poster in his room. Anime Flanderization does not help, depicting Freed unable to do anything without wondering what Laxus would do first.
Mirajane x Jenny: Chapter 279, Mira looks forward to seeing Jenny naked. After Natsu destroys the building everyone is in; Jenny, who thanks to Mira is naked below the waist, and Mira, who thanks to Jenny is naked above the waist, end up on top of one another.
Erza has some lesbian tendencies, often commenting on Lucy's looks and in the anime going as far as having a doki-doki moment over her sexy lingerie.
Erza x Coordinator: In The Movie, there is quite a lot in a surprisingly short amount of time. To add insult to injury, not only Erza defeats her by wearing a bridal dress (which she can't dispel with her Anti-Magic), but Coordinator also believes that Erza just want to get married that bad.
In a special chapter Erza manages to make rogue mage, Moulin Rouge (who, as another bonus chapter revealed, was Bisca prior to joining Fairy Tail), fall for her...after beating the crap out of her. Maybe it was the head patting at the end.
Minerva has embraced full-on Foe Yay for Erza in the Tartarus arc, becoming depressed when it looked like Erza had died outside their battle, and becoming ecstatic and even referring to her as "Beloved" when they continue fighting later.
Mira and Erza also have a bit of their own Les Yay together, there's the normal kind where they are extremely close friends, even if they butted heads as kids. Then there is the weird S&M fetish they seem to have for oneanother.
Of course its no surprise by now, that Lucy got roped into their games.
Ichiya x Eve: Why did Rufus show to him a precise memory of Ichiya taking a bath to Eve?
A bit between Rufus x Gray too. Rufus seems to flirt slightly with Gray during the battle, even calling his future defeat as a "requiem" to him. Furthermore, Gray is a bit obsessed with the idea of personally defeating Rufus in battle.
Flare x Cana: Flare uses her Prehensile Hair to restrain Cana and then give her a bath, making sure to "clean every nook and cranny".