On A Cross And Arrow is a My Little Pony: Friendship Is Magic fanfiction by Conner Cogwork.Twilight Sparkle and her friends have planned a day trip to Manehattan, using a new teleport spell Twilight's been studying. Unfortunately, due to a slight mix-up the girls are instead sent to... Ponyville. It's not the Ponyville they know, however, but one in an alternate universe where everpony's genders have been switched. Now the girls have to figure out how to get home without drawing too much attention to themselves... especially the attention of their counterparts in this dimension.A voice drama is in production. See here for more information. A fully voiced reading of the entire series can be found here. Can also be found at Fanfiction.net and FiMFiction.Cogwork has also written a sequel, On A Whisper Of Wind, where Applebuck travels to the mane 6's universe to find his "cousin" again.
Bi the Way: Dash and her counterpart Blitz are both secretly bi-curious. Elusive also gives a hint of this with some off-hand thoughts towards his masseur.
Twilight Sparkle and Dusk Shine both start crushing on the idea of each other's mentors. It's never stated outright if they feel the same about their own mentors, but they do touch on the idea of admiration easily turning into love, so the possibility is definitely there.
Celibate Hero: Even to the point where Twilight felt extremely awkward about sleeping in her gender-swapped version's bed. See Sleep Cute below.
Chivalrous Pervert: Elusive to an extent. He rather blatantly eyeballs Rarity - particularly her flanks - and primly compliments her figure in a way that Rarity knows is code for "you're hot." But of course, he's nothing short of a gentlecolt to her. Obviously, being technically the same pony, the same goes for Rarity in a rare female example of the trope.
Double Take: Elusive and Mrs. Cake from seeing Berry Bubble followed by his double, Pinkie Pie.
Female Gaze and Male Gaze: When first meeting Elusive, Rarity inwardly compliments how his cutie mark is set upon "such firm cheeks," and seems delighted over the length of his horn. Likewise, when she's invited into his boutique, she struts in to show off and begin seducing him, and is "not disappointed, as she felt eyes upon her flanks."
Male!Applejack comments that he's noticed Dusk Shine looking at his older sister (which probably means that Twilight Sparkle has been admiring Big Macintosh, as well.)
Follow the Leader: While not the first piece of fiction to have gender-flipped ponies, this story did open the floodgates for many other stories involving the gender-flipped Mane Six, and has given the gender-bent ponies their fanon names: Dusk Shine, Elusive, Butterscotch, Rainbow Blitz, Applejack, and Berry Bubblenote counterparts to Twilight Sparkle, Rarity, Fluttershy, Rainbow Dash, Applejack, and Pinkie Pie, respectively.
Fanon Osmosis failure: This was the fic that locked in the Fanon names for the gender-flipped Mane Six, EXCEPT for Pinkie Pie, whose counterpart is here named Berry Bubblenote Short for Beriswainer Da Vinci Bubble, just as Pinkie's full name is Pinkimena Diane Pie while at least half of the works that take the rest of their names from On a Cross and Arrow flip his to Bubble Berry.
Not technically one of the Mane 6, but Spike's counterpart here is named Spines, while nearly all of the copycats call her Barb.
She keeps it up for most of the fic, not sure what them interacting will cause. A majority of it appears to be her being just plain scared of meeting her alternate selves.
Noodle Incident: Applejack mentioned a time Rainbow Dash got stir crazy from being coped up too long. Apparently it wasn't pretty.
Spines brings up the poison joke incident when they recount Butterscotch's (actually Fluttershy's) strange behavior, referring to him as "Butterbabe". Presumably Butterscotch was cursed with a very sexy female voice that time?
Oh Crap: Everypony's reaction to the chaos that would be created if Pinkie Pie and her counterpart Berry Bubble collaborated on a party.
Also to the realization Rarity has tricked them so she can go see Elusive.
Palette Swap: Apparently Mr. and Mrs. Cake's gender-swapped selves are just each other's body shapes with their natural colors. Applejack is shocked to see this.
Rule 63: The plot focuses on the canon characters meeting their opposite gender selves.
Screw Yourself: By the end of the fanfic, half the Mane cast is in love with their opposite gendered self. It's also implied the same between Celestia and her male self Solaris as well—though in that last case, it's difficult to tell, since they could just be trolling each other.
Sequel Hook: The last chapter of Cross and Arrow set up and is the prologue of Whisper of Wind.
Ship Tease: Many of the ponies find themselves attracted to the opposite-gender counterparts of the ponies they are often shipped with. (Rainbow Dash towards Berry, female Applejack towards Rainbow Blitz, Twilight and Dusk towards their mentor's gender-swapped selves, etc.)
There's also the fact that Celestia and Solaris do some light flirting at the end of the fanfic.
Depending on how far you want to look into it, every possible two-pony combination of Dash, Blitz, and both Applejacks is also teased.
Pinkie Pie: I've heard a lot about Sugarcube Corner and I've always wanted to come visit, but I've been busy being kept in a cave, so I havenít had a chance until now to visit! I'm so glad to finally see the place, even if it may be like I HAVE seen it all before, but that would be silly, it's not like I fell out of a dimension that's just like this one, save that everypony's genders are opposite, right?