Time travel, you say...
?
ZELDA, you say?!
Now this is a discussion that I simply cannot stay out of!
First off, I'd like to bring some outside facts to this conversation. Information gleaned from LoZ: Windwaker's opening sequence suggests he broke free, many many many years later.
Windwaker's Prologue
The boy's tale was passed down through the generations until it became legend...
So, now, as the question was put, just when WAS he sealed?
Very likely, he was sealed
outside of time - thus ceasing to exist in the time-flow. Because the sages were not
in time in any visible manner, but rather set apart in a place that certainly did not seem to be Hyrule.
Also, Link, that same Link that slew Ganon, left on another adventure into another place (another world, another country perhaps)
when he was a child. Thus is was without fear that he left, without worrying about what would become of Hyrule. This indicates that there was no longer any Ganondorf to worry about. If not, very likely he would have stayed to prevent this danger from occuring. Also, Saria was not there (it was stated he left, looking for a friend in Majora's Mask) so it can be assumed that she was also gone, directly out of the flow of time. Thus it is safe to assume that Ganondorf as well was taken out of time, and sealed out of time.
mrgreen 
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