My opinion is that while Chrono Trigger is a better game on the whole, I enjoyed Kingdom Hearts more. How do I know this? I still haven't managed to finish Chrono Trigger, but have played through KH four times.
Nah, what really irks me is that Crash Bandicoot (and/or its two sequels), Spyro the Dragon (and/or its two sequels), and Sly Cooper (and/or its two sequels) have not made the list at all. I daresay I would gladly remove a few titles (Kingdom Hearts 2, Sonic the Hedgehog) in favor of the former trilogies.
For the record, I suppose I'll list my top ten favorite games, limiting each franchise to one spot (note that after position 5 or 6, the order in which I like the games gets slightly hazy and unstable, and is largely dependent on my mood).
1. Crash Bandicoot 2: Cortex Strikes Back
2. Sly 2: Band of Thieves
3. Spyro 2: Ripto's Rage!
4. Uncharted: Drake's Fortune (Undoubtedly, Uncharted 2 would occupy this space if I had played more of it than the demo available on the PSN Store)
5. Jak 2
6. Ratchet and Clank: Going Commando
7. Metroid: Zero Mission (Has the most solid physics, along with Fusion, but allows for sequence-breaking)
8. The Legend of Zelda: The Wind Waker (Is Ocarina of Time that much better? Anyway, haven't played that one either, at least, not past Dodongo's Cavern)
9. Super Mario World (I'm honestly not sure whether I like SMW, SMG, or SM64 better, so I'm letting the nostalgia factor tip the scales; SMW is the only one of these I played before the age of ten)
10. Kingdom Hearts: Re: Chain of Memories (Had the best mix of strategy and real-time battle; 358/2 Days deserves honorable mention as far as the KH series goes)
Also, you may notice a trend as to which games in their respective series made the list...