If he got lost in the forest and became a stalfos, it would possibly explain his skeleton-like appearance in
TP. Not that he couldn't have looked like that just because
he was dead, but there are always other possibilities.
I think that the Saria's Song piece that plays on the very last screen of the game (the 'The End' screen) suggests Link's voyage ended successfully, though, so I guess another possibility is that he went back to Hyrule with Navi (assuming she came back for him) and lived happily ever after drinking milk and cutting grass (professional lawnmower, maybe? The job pays for itself) and doing whatever he wants. Maybe he got with the Princess and kept Malon as his mistress.
It'swhatIwoulddo.