Predictable, but - the kiss in XF. The tension between Mulder and Krycek throughout the scene, the kiss on the cheek, and Mulder just sitting there, stunned.

Voyager: that scene in The Chute where Harry and Tom huddle/sleep in their little hut and there's clutching/holding of hands.

and probably a lot of other things that I'll remember once I've posted this. :)