JuicieJ
SHOW ME YA MOVES!
Gonna put my two cents in again.
Let's look at some reasons, that to me, make it so that it's gotta be Navi and not Saria.
1. Right after the MM intro when it says "in search of a lost friend" (or something along the lines of that) it plays a fairy noise.
2. Navi leaves Link immediately after OoT, and Link heads to the castle courtyard to warn Zelda with the Triforce of Courage in hand. This would mean that this time would have to be atleast after Link receives the Kokiri Emerald to fill Zelda's prophacey (slaughtered that spelling I know it xD) meaning the Great Deku tree is dead, so why would Navi head back to her old dead friend? The only other place she would likely be is in the Lost Woods, (fairies aren't found outside the forest, atleast not the ones like Navi, so non-healing fairies).
3. The Forest Meadow is Saria's hang out spot. So if she's not in the village she's there right? Heck she went there so often that a town member tells you that she's in the usual spot, so why would Link get lost? And Saria doesn't enter the Forest Temple until Ganondorf comes to power and she hears a voice crying from inside. Makes it very unlikely Saria would be lost, or missing in general.
Have a few more things, but I think this just about covers the gist of it. Again just my two cents.
We don't even know if he was in the Lost Woods. I think the guidebook said he was (the official Nintendo guidebook, not Prima or anyone else), but even if it didn't, it does make the most sense that it was deep in the Lost Woods. I mean, what other forest had we seen at the time?