OK, I've found somethink in this walkthrough:
http://www.ign.com/faqs/2003/chrono-trigger-walkthrough-437178.
Here it says:
MECHANICAL ENEMIES: Lucca's Plasma Gun (found in the Factory) might
inflict Stop-status to the following enemies: Bug, Bugger, Byte,
Cybot, Debugger, Debuggest, Martello, Proto 2, Proto 3, Proto 4,
Synchrite.
MAGICAL ENEMIES: These enemies have magical properties: Barghest,
Blue Scout, Egder, Jinn, Jinn Bottle, Juggler, Krakker, Mage, Nu,
(Octobino,) Red Scout, Scouter, Sorcerer. The following weapons are
effective against them: Demon Edge (150%), Pearl Edge (150%),
BraveSword (200%), Masamune (2) (200%), Demon Hit (200%).
It doesn't say anything about the DS enemies, although I suppose they can be deduced from this. I guess the complete list would be as follows:
Mechanical enemies: Bug, Byte, Cybot, Deverminator, Deverminator EX, Exterminator, Iron Maiden, Martello, Prototype, Synchrite, Version 2.0, Version 3.0, Version 4.0.
Magical enemies: Blue Scouter, Blood Yolk, Chaos Mage, Djinn, Djinn Bottle, Egg Ooze, Ghul, Jackpot, Juggler, Nu, Red Scouter, Scouter, Sorcerer, Zealot Mage.