This is a really hard topic for me to answer with any sort of unbiased response. I'll be frank, while I was playing through Majora's Mask this week, every time I saw/talked with Romani and Cremia, my heart would just melt and I wanted to give them a big hug. But that's Majora's Mask and this is Ocarina of Time so I'll get off that.
I have to make a second admission, it's hard for me to be unbiased in terms of Malon because even before I played the game I have always been extremely attracted to girls with red hair and green eyes, and I'm a big fan of long hair. Malon, for me, represented one of those girls I'd always wanted to meet/hook up with. So no matter how much might like any of the other girls, Malon's always gonna get that +5 cuteness, etc.
That said, I have to admit that I find adult Ruto to be extremely sexy and Saria to be extremely cute. I really can't comment much on Zelda because.. well, I honestly didn't care much for her design in Ocarina of Time. She's beautiful grown up, yes, but for me it doesn't hold a candle to her Link to the Past incarnation or most of her others for that matter. Zelda in Wind Waker is so adorably cute I just wanna hug her, and Twilight Princess Zelda is beautiful and down-to-earth looking. That's actually one of the things I liked about TP; the muted colours used kept everything from being all bright and flashy and colourful which was a good change from Wind Waker.
The subject of Impa.. ugh, I'll be flat out honest here. I've never been an Impa fan in any of her incarnations. She was originally an ugly old woman, then she became this like.. buff body-builder "dike" looking character, and later she turned into this fat cheerful woman. I will say she's the most diverse out of all of them. :p
Then there's Nabooru... how do I even start. I think she's beautiful, yes, but all the Gerudo's are cute/beautiful to a degree. The thing that's always bugged me about the Gerudo were the big mouths and noses, they felt exaggerated. So it's really hard to say. The Cucco Girl (or Anju if you want to give her a name) is certainly cute and I'd love to hang out with her, but for me her design is a water down Malon. Now you look at the artwork, though, and her real beauty and charm come out.
I guess that's the problem, really. You look at the video game versions of these people and you have to ask yourself: Yes, this is a 3-D pixelated, slightly blocky character... so am I attracted to them? Most of the girls I'd have to say yes, a few I'd have to say no.
1) Malon (child or adult, she's adorable and sweet and I will always love her)
2) Adult Ruto's sexyness ties with Saria's cuteness
3) Adult Zelda's beauty is mirror'd in Nabooru's sultry appearence
4) The Cucco Girl
5) The like.. NPC girls who run games or are secrateries (you see them more in MM, I think)
Oh and I just realized that the thread specifically says "cutest female", so I'd have to flat out say Malon.