It is all over the My Little Pony fandom.At this point, it is fair to say that everyone in the main cast has been paired with everyone else multiple times over. In the early days of the fandom it was Rainbow Dash that tended to get paired with others, due to the perception that she was a lesbian. This perception has now faded a little, and now there are few differences to the other cast members in the type and number of ships she is involved in. Due to the diversity of shipping among the main cast, the only ships that can be singled out as legitimately influential are among minor characters. If Octavia and DJ-Pon3 are being shipped it is normally with each other, for the same reasons that they are depicted together in non-shipping works (ie, their complementary themes). Colgate and Berry Punch are also relatively exclusive to each other, due to their scene in Winter Wrap Up where they were seen nuzzling. Interestingly, the shipping of Doctor Whooves and Derpy Hooves has recently stepped up in numbers.
In addition, many fans (emphasis on 'many') like to (in some form or way) 'teleport' either themselves or their own created characters (human or pony) into the world of Equestria and, eventually, ship themselves or said characters with many different ponies (varying from Princess Luna to the main six to several background ponies).
It is Lyra and Bon Bon who take the prize for the most pervasive, most exclusive ship however. Paired up very early on due to often appearing together, the ship was solidified when they were spotted eating together in Swarm of the Century. Since then they have almost always appeared together and been depicted as romantic partners, with impressive amounts of fanart and fanfiction (and at least one song) dedicated to them. Hasbro appears to have noticed, as Lyra and Bon Bon, and Colgate and Berry Punch are both shown standing together in the Comi-con Poster. As hinted above, most pairings are female/female simply due to the majority of major characters being female. Due to this Big McIntosh and Soarin’ (and Snails oddly enough) have been seized upon by fans of straight pairings, as they are some of the few prominent male characters on the show