Crono, Magus, and Ayla. By the time you get to where you're ready to fight Lavos, you should have amassed a ton of gold and elixers and other healing items. Give Crono and Magus Gold Studs and watch the game kick into easy mode.

Crono, Alya, Lucca.


Crono: Luminare spam.
Ayla: Spam Critical hits for 9999 damage, Dragon's tear REALLY helps. (To get 9999 damage Critical hits, Get Ayla to level 91 or so, When her fist becomes bronze knuckle, Critical hits deal 9999 damage)
Lucca: Flare Spam

If you're going to spam ultimate magic attacks, Crono, Magus, and Lucca would be a better choice, though you'll lack reliable healing techs. Not that it really matters when you're dealing 6000+ damage every turn though.

Robo, Ayla, Crono; insane damage and Robo is a pretty good healer when needed.

I plan on using Crono, Lucca and Marle in the future.

Right now, I'm running Crono, Lucca and Robo. Crono will spam Luminaire or Frenzy for massive damage while Lucca spams Flare, Dual techs with Robo or Wondershot. Robo's main purpose is to heal.

Crono, Frog, Marle for last play through.

Crono, Frog, Ayala/Robo this time. Any objections/helpful advice?

At the endgame, my favored combo is Magus, Robo, and Alya. Robo for healing, Alya for physical attacks, and Magus for spell spamming. I like to be able to fall back on something if what I'm doing doesn't work.