OK, Chrono trigger used changes in time periods to good effect in the plot, but I noticed it much less as a gameplay mechanic. There were a few moments, like putting that ladder up in the mountains, but for the most part it was just for major plot developments.
In -gameplay-, definitely a nod to the Oracle of Ages and Seasons. Ages used it better, but that's not really a surprise since time was the significant force there. If they had more engaging writing (like Chrono Trigger, for instance...) it would have probably had a greater emotional effect to see the bridge you helped to get built standing hundreds of years later, Rafton's grave, the peaceful village atop the volcano. It doesn't quite work since Link is kind of a faceless lump in the Oracle games, but oh well.
Day of the Tentacle was partly fun because figuring out how to get things from one time period to the other was really neat if sometimes infuriating as hell. Even when the answer was something absurd I had to love it because it was brilliant at the same time. Sort of like Dr. Who now that I think of it.
I know the time mechanic in Majora's Mask isn't gameplay, but I liked what it did to the atmosphere, putting you in a sort of twilight zone. Every three days you go back to the beginning and no one remembers you, you walk through places you've been, speak to people you know, whose heartbreaks and triumphs you've seen and participated in. But they don't know you. Like everyone else in the world just has this blip in their memory and you're either the only one left sane or the only one who's gone mad.
The time control in Braid LOOKS hypnotic, but I'm pretty sure I could make it through maybe...four or five pathetic attempts at the first level before I gave up. It's a really neat concept, but it looks way harder than I would have the patience for.