Well Superman and Batman TAS, go without saying. I'd add:
Captain Planet: When other kids were watching Sailor Moon, I'd be watching Captain Planet. Molded my young mind and made me the ecologically concious person I am today
Swat Cats: This cartoon ROCKED! And I don't mean just that it had a kickin soundtrack, it was just a real fun toon to watch
Pirates of the Black Water: Interesting animation, great story and just all around memorable cartoon.
Shadow raider War Planets and Reeboot: Both from Mainframe animation. I still have most of Reboot on some dvd's somewhere. It was just so funny and ahead of its time
Beast Wars: Amazing. Period. Dinobot is my favourite character and one of my all time favourite robots.
The X-men. Spiderman and Iron Man cartoons: Main reasons I read comics today to be honest. :)
Have to think of more stuff but that's it for now... :)