I'm a huge huge HUGE fan of AlmiaShipping. :3
Although I've never read the Shadows of Almia manga, I ship them like hell anyways.
One obscure ship I like is RangerTeacherShipping (Ms. April/Mr. Kincaid). Don't ask me why, I've just always liked that ship, and it doesn't get any love from what I can see.
I also think RedrangerShipping (Summer x Red Eyes, Pokémon Ranger: Guardian Signs) needs more love. And maybe it's just the shipper within me, but I swear Ben seemed jealous after Red Eyes became good or whatevs.....:3
I'm also a fan of BlackmaidenShipping (Silver/Dawn, game), CircleOfFriendsShipping (Solana/N, Game), RubyShipping (Lucas/May, game again) and TeaShipping (Daisy Oak/Bill, games).
ALL of those need more love. :D