I was watching DeadAlive yesterday and after Scully says "Have you any idea what you've been through?" and Mulder says "Only what I see in your face", it looked to me like Mulder mouthed 'I love you' to Scully. This may be my eyes playing tricks as I'd not picked up on that before. I would have wound it back straight away to check but I was watching it with my Dad and didn't want to come off as too much of a crazy shipper person! :-P Will check it again tonight.
I know there was a similar rumour about the moment in the film where Mulder gives Scully mouth-to-mouth and she says "I had you big time", but I listened to that quite a few times and am fairly sure Mulder's just exhaling! Am interested if anyone else has picked up on the DeadAlive one though. But, like I say, tis probably just in my head!