Well, I chose the Masamune. I liked the Mystic War story arc more than any other part of the game, so I guess I'm biased. But I'll rate some of the others:
Epoch: Yes, important, but not the most important. Main purpose, story wise, was to get back to the Dark Ages, and after that, not essential to the story.
Masamune: I'm going to try real hard to look past my biased-ness. The Sword that could defeat Magus, and the Sword that defeated the Mamon-machine, actually causing the Ocean Palace distaster. Past that, its not much more important...
Chrono-Trigger/Time Egg: Actually, pretty low on the list. You can beat the game without it.
Ocean Palace: To me, this seems a bit out of place. A very imporant event did take place there, but that event could have taken place back at Zeal. The only thing that made it special was that it was considered closer to Lavos.
Mammon Machine: Very important for the Zeal story arc. It was this and the Masamune that caused the Ocean Palace disaster.
FATE/Chronopolis: Well, agian, my biased-ness got me here too. I'll try to overcome it. Of all the inventions, this was the most imporant (by far) for CC.
Pendant: Well, kicked the series off, didn't it? Very important. I predict it will win.
Sapling of Hope: What exactly did this do? Restart the growing of vegition after the dark ages? Meh, more important for the Chrono-world than the story.