Diana Fowley/Mulder -- they were together before, but she helped Mulder when he was sick... bringing forth that whole bed scene (yes a bad fever dream) of him and her having sex
Scully/Fake Mulder (Eddie Van Blundht) -- the whole scene of Scully almost kissing him and Mulder walking in on it
Mulder/1930's Scully -- we get a kiss, but then she punches him; and don't forget the 'I love you' Mulder says to her (the present day Scully) and her 'oh brother' back to him -- hate that scene
Scully/and the guy from Never Again -- strongly hinted at
Tad being hinted at with Scully (thankfully nothing came from that)
Scully and the Were-Monster in the Were-Monster's dream -- very strongly making out
Mulder and Agent Einstein in a scene where she dominates him (she's dressed up in a dominatrix out fit) -- Mulder was stoned at the time... on Niacin /facepalm
Basically /other stuff happened more than enough on the XF. Basically kind of taunting shippers. Closest we got was with IWTB (thank alien for Frank), The Truth (thank alien for Kim Manners), Existence, Millennium and All Things.
Everything had to be uber implied. It's why I'm no fan of Plus One. It just taunted and teased shippers. I have no time for that.