Which faction are you? Which GC and tech level?

He is best killed using massive waves of fighters and bombers, probably backed up towards the end by powerful capital ships with lots of turbolsers and ion weapons. Heroes might help given their bonuses but use them very carefully.
A cap ship heavy fleet can work but will take heavy losses.

Its often best to kill him on defence, preferably with an ion cannon if rebels. If you do attack, try to get him alone or with minimal escort. It may be worth hitting and running to whittle down an escort fleet, or stealth raiding the planet to remove any stations or planetary turbolaser.

This said, ideally you would prevent him from being built in the first place (since there is a timer and a finite number of possible build locations).

You could also consider just not fighting him, and attacking where he isn't. Its a big galaxy, and the Executor can only be in one place at once.