I voted for Milagro because I love the angsty/shippy stuff. Plus the overall story just has you from the beginning. It really shows her in a light that we don't often see her in. It's also a great stand alone. I could however have a love-fest with Never Again. I love the Mulder/Scully phone conversation:
Mulder: How do you know?
Scully: What do you mean, how do I know? You assigned me the background check. I did as told, as always.
Mulder: Okay, just hold off until I get there, okay?
Scully: What, you don’t think I’m capable?
Mulder: Of course I believe that you’re capable, it’s just that in this case I need you to...
Scully: It’s not just in this case, Mulder.
Mulder: Wh-what’s the agent’s name in Philadelphia?
Scully: It is over. Done. Pudovkin is out of our hands. Look Mulder, I have to go.
Mulder: What, have you got a date, or something? (Scully doesn’t answer) Y-you’re kidding.
Mulder: Marry me.
Scully: I was hoping for something a little more helpful.