Here are point-by point guides to the Season 5 moments packed with DAL and UST. Here I've tried to capture the most important events regarding Mulder and Scully's relationship. For more comprehensive, general reviews go to my 5th Season Review Page. Enjoy.
Young Gibson tells Mulder that he's thinking about one of "the girls", and one of them is thinking about Mulder too. Right then, Scully's eyes widen and roll upwards almost imperceptibly, like someone who's been caught cheating on her diet. Surely Scully was the one thinking about Mulder. ;-) Then Gibson tells Mulder that the one who's thinking about him doesn't want him to say. That's Scully, hiding her feelings. Later, Gibson busts her again wondering about "that girl"--Fowley. Scully is really disturbed about the possible threat to her relationship with Mulder.
When Scully glimpses Mulder and Fowley and thinks they're holding hands, she dashes to her car in despair, honestly thinking that Mulder no longer loves her. You could almost read her thoughts--even though they never spoke about it, they had an understanding that each of them always comes first in the other's life. Now Scully believes Mulder has broken that trust. In a delightfully catty move, she calls Mulder and insists that they meet at work in order to split up Mulder and Fowley for the moment. ;-)