Shipping: Gerund of 'to ship'.
(to) Ship: Comes from 'relationship' and (I believe) the Star Trek fandom. To ship is to hold faithfully to a pairing [read: fan-deduced theory of a couple] of two (or more) characters.
Related words
OTP: Literally, "one true pairing". The ship that a fan holds above all others and will not break up for anything, including blood, love, money or crack.