There definitely aren't many. I'd say:
Elena Fisher (Uncharted series): She's relatively real, she has normal proportions, she has fear, excitement and anxiety and, whilst it could be argued that she's portrayed as being relatively perfect, she still has very human flaws and traits. She runs off ahead (which could put her in danger), she has stubborn and even reckless moments, but you never lose the feeling that, if she actually existed in real life, she would be exactly the same, and act in the same way.
Chloe Frazer (Uncharted 2): A little more realistic than Elena, in my opinion, in terms of being more complex and not just all bad or all good. She reacts as most people would, wants to save her own life and is angered when obstacles are put in front of her. She's sexy, but that sexuality doesn't get in the way of her doing her job, and she's conflicted on more than one level.
Trip (Enslaved): Again, real in the sense that she's not all bad or good, but a mixture of both at various times, which reflects normal people. She feels guilt over enslaving Monkey, but knows it is a necessary evil so that she can get back home alive.
All of these women are realistic in terms of body proportions (obviously Chloe has a bits of a butt and larger breasts than the other two, but you know the girl works damn hard for her body and she's not out of the realms of possibility in terms of being 'real') and emotional burden. All 3 show a range of emotions.
On that note, and I might get flamed for this, but I also think that Bayonetta is quite realistic to a certain extent. Not in terms of body proportions, but when she finally begins to show emotions, they're quite real. Her mothering of Cereza soon becomes realistic, and when she lets her vulnerabilities show, she becomes much more human than the elusiveness and confidence/arrogance she portrays throughout the game.
However, Chloe, Elena and Trip are the most realistic in general (body AND emotions). I also agree with the poster who mentioned Bonnie McFarlane.
If I think of any more I'll come back.
This is a great topic, OP! It really made me rack my brain trying to think of an answer. There really AREN'T many realistic women in games, are there??