Personally think Chell would win, especially after Alyx's new injury
Chell could... run away the best, or drop some heavy cube from the ceiling onto Alyx, or possibly just fall on her head herself, since she can fall from any height... however, Falling Objects < Explosives.
"You go ahead Gordon, I'll cover you from here."
Fuck that, if you want to come with me you best be killing as much shit as I am, but NOOOOOOO, Alyx always wants to stay behind next to the turret and leave me running all kinds of perilous mine shafts and toxic waste infested canals.
I wish I could change my vote after thinking about this. Chell would kick Alyx's ass. Look at the facts. Alyx was SAVED by the GMan and then after she died in episode two she was SAVED by the vortigaunts and throughout the series I had to constantly save her ass.
Chell on the other hand, single-handedly defeated GLaDOS with a gun that doesn't even shoot bullets. Props.
But chell only beat GLaDOS cos her only defence was a stupid turret.
but saying that I still think that Chell would own Alyx, portal under her feet, portal on building 20 ft up... one dead Alyx
I said nothing about DOG, DOG should be left out of this fight, hes taking care of those advisor slugs
.
Chell would fall on her ugly face 
.
Portal into acid ftw!
But this is not a popularity contest is it? Fair enough.
All I can think of is the moment I first met Alyx, where she had just single-handedly taken out a room full of combine.
(ep2 spoiler)
Sure, she had to be saved by the vorts in ep2, but come on, she got STABBED TWICE IN THE BACK, QUITE DEEPLY INDEED. You think Chell wouldn't also need the Vorts to save her from that?
Plus, did you see that when she did that wrestling move on that zombie? and when she booted that ant lion in the head and shot it while her heel was still in its face? That was so cool!
What's Chell got? A portal gun. That isn't hers. That only works on certain sufaces. That may not work at all after portal's finale. Oh, and she doesn't take falling damage.
Ok then, FIGHT!
Chell looks up for somewhere to fire a portal into.
Alyx kicks her in the chin, knocking her unconcious.
Wow, that was quick.
Anywho, Alyx would only win if she was naked.
Double knock out. 
or was it just me...
Crooked Paul wrote:
If you listen to the commentary track of Ep 2 they talk about how they changed a lot of her clothes, like the cut of her jacket and her belt. Of course you guys noticed the panties first.
I want a Black Mesa hoodie like she has so badly.