Here is a list of all it had by year. Some of these stayed and some were replaced. DBZ was never replaced the entire time.
1997
ThunderCats (TV-Y7-FV)
Cartoon Roulette (composed of Space Ghost, Birdman and the Galaxy Trio, The Herculoids, Mightor, Shazzan, Teen Force, The Impossibles, and the 1940s Superman) (TV-Y7)
Voltron (TV-Y7-FV)
The Real Adventures of Jonny Quest (TV-Y7)
1998
Robotech (TV-Y7-FV)
Beast Wars: Transformers (TV-Y7-FV)
Sailor Moon (TV-Y7-FV)
Dragon Ball Z (TV-Y7-FV, TV-PG-V for episodes containing language and gruesome violence)
Superfriends (TV-Y7)
1999
ReBoot (TV-Y7-FV)
The Powerpuff Girls (TV-Y7-FV)
Ronin Warriors (TV-Y7-FV)
2000
G-Force: Guardians of Space (TV-Y7-FV)
Gundam Wing (TV-Y7-FV) and (TV-PG)
Tenchi Muyo! (TV-Y7-FV)
Batman: The Animated Series (TV-Y7-FV)
Tenchi Universe (TV-Y7-FV)
Tenchi in Tokyo (TV-Y7-FV)
Blue Submarine No. 6 (TV-Y7-FV)
Superman: The Animated Series (TV-Y7-FV)
2001
Outlaw Star (TV-Y7-FV)
The Big O (TV-Y7-FV)
Cardcaptors (TV-Y7-FV)
Mobile Suit Gundam (TV-Y7-FV)
Gundam 08th MS Team (TV-Y7-FV)
Dragon Ball (TV-Y7-FV)
Batman Beyond (TV-Y7-FV)
Zoids (TV-Y7-FV)
Gundam 0080 (TV-Y7-FV)
2002
Hamtaro (TV-Y) and (TV-G)
Classic Zoids (TV-Y7-FV)
G Gundam (TV-Y7-FV)
He-Man and the Masters of the Universe (TV-Y7-FV)
Transformers: Armada (TV-Y7-FV)
G.I. Joe (TV-Y7-FV)
Samurai Jack (TV-Y7-FV)
2003
.hack//SIGN (TV-Y7-FV)
Martian Successor Nadesico (TV-Y7-FV)
Gigantor (TV-Y7-FV)
Neon Genesis Evangelion (TV-Y7-FV)
Dai-Guard (TV-Y7-FV)
YuYu Hakusho (TV-Y7-FV)
Rurouni Kenshin (TV-Y7-FV)
Justice League (TV-Y7-FV)
Cyborg 009 (TV-Y7-FV)
Superior Defender Gundam Force (TV-Y7-FV)
IGPX: Micro Series (TV-Y7-FV)
Dragon Ball GT (TV-Y7-FV)
Star Wars: Clone Wars (TV-Y7-FV)
2004
Duel Masters (TV-Y7-FV)
Astro Boy (2003) (TV-Y7-FV)
Transformers: Energon (TV-Y7-FV)
Jackie Chan Adventures (TV-Y7-FV)
Gundam Seed (TV-Y7-FV) and (TV-PG)
Megas XLR (TV-Y7-FV)
Rave Master (TV-Y7-FV)
Teen Titans (TV-Y7-FV)
Justice League Unlimited (TV-Y7-FV)
2005
D.I.C.E. (TV-Y7-FV)
Zatch Bell! (TV-Y7-FV)
The Batman (TV-Y7-FV)
One Piece (TV-Y7-FV) and (TV-PG-V)
Transformers: Cybertron (TV-Y7-FV)
Yu-Gi-Oh! (TV-Y7-FV)
Naruto (TV-PG-V,D)
Bobobo-bo Bo-bobo (TV-Y7-FV) and (TV-PG-D)
IGPX (TV-Y7-FV) and (TV-PG-L)
2006
Wulin Warriors (TV-Y7-FV)
Pokémon Chronicles (TV-Y7-FV)
Fantastic Four: World's Greatest Heroes (TV-Y7-FV)
Pokémon: Battle Frontier (TV-Y7-FV)
Yu-Gi-Oh! GX (TV-Y7-FV)
MÄR (TV-PG-V)
The Prince of Tennis (TV-PG)
2007
Storm Hawks (TV-Y7-FV)
Mega Man Star Force (TV-Y7-FV)
2008
Bakugan Battle Brawlers (TV-Y7-FV)
Blue Dragon (TV-Y7-FV)
Ben 10: Alien Force (TV-Y7-FV)
2012 (April Fools' Day Stunt)
Astro Boy (1963 series (TV-PG)
Bleach (TV-14 V)
Trigun (TV-14 V)
Source: Wiki and my mind.