It's been bothering me for quite a while how many people believe the sparkle to be Crono's soul during his death scene, (Especially on the GameFAQs forums *shudder*) so I've decided to set the record straight here as to why it is undoubtedly not.
The confusion was never an issue before those neat little anime cut scenes from the PSX version came into existence. During the SNES/SFC days it was quite unanimously agreed to be the pendant. Shiny little sprite rises up from his body, pendant is found by party member X later. 1 + 1 = 2, no arguments.
Then in the pretty new anime scene we see... Strange glowing ball rises, Crono gets dusted, pendant is found by party member X later. Suddenly we have ? + 1 = y... I'll mention now that I fucking hate the individual who planned out that scene...
In my opinion, the animators made the item rising from his body correspond with the spritework on the screen without actually confirming what the sparkle was representing. They see a sparkle rise, they animated a sparkle rising, no added details in that scene.
Now suddenly a large amount of people think it was Crono's soul, or some energy ball from Lavos, maybe a passing UFO that emerged from a dimensional rift in Crono's shirt, who knows. It's horribly ambiguous.
One thing I can state for certain though, is that it is not his soul. The reason is evident when the party gets Crono back.
In the time freeze where they switched his body with the Dopple Doll, the sparkle was still there above his body. Thus, when they pulled him out, the sparkle stayed behind. This makes the most sense if you presume it was the pendant, so it is still found on party member X's shoulder later and their own past remains unaltered. (Don't give me that TTI crap, paradox's can happen to time travellers, otherwise there would be no damn point in using the doll in the first place!)
Now if they pulled back Crono and it was his soul represented by the sparkle it would still remain in the past to be destroyed. Now I know he doesn't talk much, but I'm pretty sure Crono, post time-egg, had his soul still intact.
In a nutshell,
Sparkle rising from Crono during death scene = Soul = WRONG!