Definitely Haruka/Michiru aka Uranus/Neptune!! I think their relationship is just so sweet and touching, I love seeing them together. I watch S and Stars just for their relationship, lol. They're one of my all-time favorites in anime.
Other ships I like... Usagi x Mamoru I like in the first season and the Ail/Ann Arc, afterward, though, it just begins to piss me off as Mamoru becomes more and more of a useless dimwit. Naru/Umino is cute. Luna/Artemis is cute. I like Rei/Yuuichirou. Usagi x Seiya is okay, I can't really see Usagi ever returning Seiya's feelings, though. As far as non-canon yuri couples... I like Usagi x Rei and Rei x Minako in the manga.