For this discussion, we are including both theatrical cartoons and made-for-TV cartoons. My choices are (1) the Superman Fleischer theatrical shorts
and (2) BATMAN: THE ANIMATED SERIES.

The nominees (in alphabetical order) include:

THE ADVENTURES OF BATMAN (1969)
THE ALL-NEW SUPER FRIENDS HOUR (1977)
AQUAMAN (1968)
BATMAN & THE SUPER 7 (1980)
BATMAN/SUPERMAN HOUR (1968)
BATMAN/TARZAN ADVENTURE HOUR (1977)
DEFENDERS OF THE EARTH (1986)
FANTASTIC FOUR (1967)
THE INCREDIBLE HULK (1984)
THE INCREDIBLE HULK (1996)
THE INCREDIBLE HULK/AMAZING SPIDER-MAN HOUR (1982)
JUSTICE LEAGUE (2001)
JUSTICE LEAGUE UNLIMITED
THE KID SUPER POWER HOUR WITH SHAZAM (1981)
MARVEL ACTION UNIVERSE (1988)
MARVEL SUPERHEROES (1966)
THE NEW ADVENTURES OF BATMAN (1977)
THE NEW ADVENTURES OF FLASH GORDON (1979)
THE NEW ADVENTURES OF SUPERMAN (1966)
THE NEW FANTASTIC FOUR (1978)
THE PLASTIC MAN COMEDY-ADVENTURE SHOW (1979)
SPIDER-MAN (1967)
SPIDER-MAN (2003)
SPIDER-MAN AND HIS AMAZING FRIENDS (1981)
SPIDER-MAN UNLIMITED (1999)
SPIDER-WOMAN (1979)
SUPER FRIENDS (1973)
SUPER FRIENDS: THE LEGENDARY SUPER POWERS SHOW (1984)
SUPERMAN (1941)*
SUPERMAN (1988)
SUPERMAN (1996)
THE SUPERMAN/AQUAMAN HOUR OF ADVENTURE (1967)
SUPER POWERS TEAM: GALACTIC GUARDIANS (1985)
TEENAGE MUTANT NINJA TURTLES (1987)
TEENAGE MUTANT NINJA TURTLES (1990)
X-MEN (1992)
X-MEN: EVOLUTION (2000)

*movie shorts

Ill agree with the Fleisher Superman shorts as far as movie cartoons go
As for TV cartoons, i'll go with the original "Batman the Animated Series" The absolute BEST animated version of Batman

I have to go with Justice League (which also included Unlimited). I was a huge fan of Batman TAS and Superman TAS and that crew of people just got better at what they were doing as time went on, JLU being the best.

JUSTICE LEAGUE (and JUSTICE LEAGUE UNLIMITED) were both very good shows.

my choice would be x-men. not x-men evolutions or whatever it is. plus its 10 times better than the films will ever be. brian singer and the director who did the third film- can't remember who it was almost ruined the francise

As as far as manga goes, I'd vote for Sailor Moon (Which is SO much better, uncut )

My favorite is:

1. the Superman Fleischer theatrical shorts
2. Spiderman 1967 version
3. The Adventrues Of Batman '67
4. The All New Superfriends Hour '77
5. Superman/Aquaman Hour '67
6. The Adventures Of Superboy '60's
7. New Adventures Of Batman '77

My personal picks would be:

The Fleischer Superman (To think of when they were made and how breathtaking and inspirational the animation remains to this day ... wow).

The Bruce Timm helmed Batman: The animated series (Outside the box animation themes with a "primetime" pacing and sensibility).

Justice League/JLU (Few shows remind me of why I loved action-animated theme shows as a child and the unlimited story potential I came to desire as an adult the way that this show does).