There are really only two couples I 'ship in my head.
The first is your bog-standard VERY reciprocated Yuyuko/Yukari.
The second is a bit of complete crack. Lily/Yuka. I just think they're meant for each other for some strange reason.
This is despite the fact I think Remi/Sakuya is pretty damn close to canon...I just still don't like it as more than master and servant.
But as for just interactions I like to see...
Yeah, SW's "entire Palace of the Earth Spirits" is probably on top of my list. So...freaking...cute...
Marisa playing off of her teammates/Kourin/Reimu is just awesome.
Yuyuko and Youmu. Complete and absolute devotion, without the need for fate hax. And Yuyu knows how to use it for maximum lulz.
Remilia in full-on Lawful Evil mode with the rest of SDM. Patchy is a bonus.
Prismriver Sisters, whether feuding or cooperating. They kinda hit the same bit on me as the SA cast, just not nearly to the same degree.
And of course we can't forget Team Science! Even if they never met, just the concept of getting Nitori, Rika, Rikako, and Yumemi in the same place makes me feel all tingly.