I'm quite fond of Navi, actually. People get sucked into the whole "Navi's friggin' annoying" mindset and miss the whole meaning of her character, the whole thing where Link was the infamous boy without a fairy and finally he gets Navi as his faithful companion. I imagine that having come from that context Link's actually quite fond of his fairy companion.
For me personally, I became kind of fond of Navi's voice from the menu of the Collector's Editon GameCube disc (my introduction to Zelda, woohoo!) where on the main menu you could press Z to open and close a little dialogue box describing whichever game or video thingy you had selected. I would press Z repeatedly sometimes just for fun. :3 It's not all the same sound effect, either - you get the standard "hey" and "listen," but some of the less used ones like "what's up" are pretty cool to hear.
It's always the voice people claim to get annoyed with, too. I quite enjoyed her appearance on-screen, floating in and out of Link's hat. There's a kind of - oh, I don't know what to call it. There's something nice to seeing Navi float in and out of Link's hat like that while playing.