I saved Cid.

I was actually playing with a walkthrough then.. it says it won't affect the ending whether you save him or not but I still chose to do it.

though I like that dramatic scene a lot too. This was actually mentioned in EGM in an issue of FF9(which is old now). It said something like those who remember "losing entire nights of sleep catching fish in order to keep Cid alive" will have nostalgia in FF9.