Someone said E.E. from MGS2 S.O.L. And while I can see that, I liked her a little because I didn't find protecting her too bad. Except for the sniping part where Snake called and ruined my shot.... And I'm a protective kind of person so I took it in stride.
I'd say that besides Navi,
Rinoa from FF8 - "I was scared, really really scared" Me - Yes I know you're a moron who hatched a half assed plan to prove herself to her daddy but let go of my thigh, I haven't finished putting on my belts yet.
I never really liked Aeris either, throwing yourself at male-protagonist is a way to make me hate you quick, fast and in a hurry. So the next entry will make a lot of sense.
Meryl Silverburg, MGS1 and 4 - I'm so tough and completely incapable, I've been desensitized to men! Snake, I totally love you after no less than ::looks at watch:: 5 hours now! We haven't spoken in 7 years but I can't stop talking about a failed relationship with someone who's closer to a father figure for me than a lover and trying to touch their face, no matter how hard they try and stop me. Oh wait, there's a man that's interested in me? Even after punching him in the face -- I'll take him instead, even if he does shit himself like a cocker spaniel.
I'm also pretty sick of whiny RPG protagonists in general and FF protagonists in particular. I'll give Cloud a pass because he was a the first that I played with seriously, but Squall was just too bitchy for me to let it go any more. But I still liked him more as a complete penis than when they made him like everyone else around him.