My friend plays as Peach in Smash Bros. While one may, offhand, assume that this is was done in a joking manner, it has become a part of our friendship (between him, a few other friends, and me, not just the two of us). "Whoop-cha!" is a common catch-phrase of ours now (the sound she makes with her -> + B move).
I often use female characters, too, but like a woman can relate to females, I, being a guy, tend to relate to guys. I usually use Marth in Smash Bros, but Zelda/Sheik is the next runner-up.
As for adventure games, I don't find women to be overly feminine, and I think the editorial over-exaggerates the incapability of Peach and Zelda. In OoT, Zelda helps you out plenty (granted, as Sheik most of the time, but it is her), and in WW she's the tough Tetra (though as a princess she's more meek, but I'd be a bit stunned if I found out I was a princess, too).
Peach, less so. However, her role is not always that of the simple damsel in distress. In the Paper Marios she is captured, yes, but she assists Mario in every way she can, taking many risks. It is very reserved, but Peach isn't exactly the best example for tough gal extroardinaire anyway. Just wanted to point out she isn't a total wimp
Someone mentioned Fire Emblem. That's undoubtedly the best representation of girls I've seen in video games, surpassing stereotpyical princess or typical RPG girls (Aeris, Tifa, whoever from FFX) and not so far off the scale of bad-assness as Samus (who is pretty much tougher than any of Nintendo's male heroes).
Anyway, I just delved far too deeply into the idea of female characters in video games, and I'm feeling a bit ridiculous (not because they're girls, but because they're video games, mind you), so I'm off to study French.