This list was compiled in 2003 and I've been hearing about it for a while. But I've only just dug the thing up, courtesy of this Russian fellow. It's easily the best top cartoons evar list I've found thus far:
1. Hedgehog in the Fog (1975, Yuri Norstein)
2. Tale of Tales (1979, Yuri Norstein)
3. Fantasia (1940, Ben Sharpsteen, Hamilton Luske)
4. The Man who Planted Trees (1987, Fr?d?ric Back)
5. The Shepherdess and the Chimneysweep (1952, Paul Grimault)
6. Future Boy Conan (Hayao Miyazaki)
7. My Neighbor Totoro (1988, Hayao Miyazaki)
8. Snow White and the Seven Dwarfs (1937, David Hand)
9. Yellow Submarine (1968, George Dunning)
10. Prince Wanpaku Slays the Great Serpent (1963, Yugo Serikawa)
11. Little Norse Prince (1968, Isao Takahata)
12. Crac (1981, Fr?d?ric Back)
13. Mr. Bug Goes to Town (1941, Dave Fleischer)
14. Wallace & Gromit in The Wrong Trousers (1993, Nick Park)
15. Spider and Tulip (1943, Kenz? Masaoka)
16. Nausicaa of the Valley of the Wind (1984, Hayao Miyazaki)
17. The Snow Queen (1957, Lev Atamanov)
18. Blinkity Blank (1955, Norman McLaren)
19. Laputa Castle in the Sky (1986, Hayao Miyazaki)
20. The Castle of Cagliostro (1979, Hayao Miyazaki)
21. Dimensions of Dialogue (1982, Jan Svankmajer)
22. The Hand (1965, Jir? Trnka)
23. A Midsummer Night's Dream (1959, Jir? Trnka)
24. Night on the Bare Mountain (1933, Alexander Alexeieff & Claire Parker)
25. Dojoji Temple (1976, Kihachiro Kawamoto)
26. The Nightmare Before Christmas (1993, Tim Burton)
27. Fantastic Planet (1973, Ren? Laloux)
28. The Magic Fox (1982, Okon Joruri)
29. Spirited Away (2001 Hayao Miyazaki)
30. AKIRA (1988 Katsuhiro Otomo)
31. Adventures of Ganba (1975. Osamu Dezaki)
31. Tom and Jerry (1965-1972, Joseph Barbera, William Hanna)
33. Astro Boy (TV) (1966 . Osamu Tezuka)
34. Father and Daughter (2000, Michael Dudok de Wit)
35. Pinocchio (1940, Hamilton Luske, Ben Sharpsteen)
36. Mobile Suit Gundam (TV) (1979. Yoshiyuki Tomino)
37. Bambi (1942, David Hand)
38. Street of Crocodiles (1986, Stephen Quay, Timothy Quay)
39. Grave of the Fireflies (1988, Isao Takahata)
40. Betty Boop (1930-1939, Max Fleischer)
41. The Iron Giant (1999, Brad Bird)
42. Cheburashka (1971, Roman Kachanov)
43. Bajaja (1950, Jir? Trnka)
44. The Sand Castle (1977, Co Hoedeman)
45. The Old Man and the Sea (1999, Alexander Petrov)
45. Toy Story (1995, John Lasseter)
45. The Old Mill (1937, Wilfred Jackson) (from the "Silly Symphonies" series)
48. Neon Genesis Evangelion (1995-1996, Hideaki Anno)
48. The Street (1976, Caroline Leaf)
48. The Snowman (1982, Diane Jackson)
51. Jumping (1984, Osamu Tezuka)
52. Heron and Crane (1974, Yuri Norstein)
53. The Emperor's Nightinggale (1949, Jir? Trnka)
54. Monsters, Inc. (2001, Pete Docter)
55. When the Day Breaks (1999, Wendy Tilby, Amanda Forbis)
56. Heidi, Girl of the Alps (TV) (1974. Isao Takahata)
57. Inspirace (1948, Karel Zeman)
58. Creature Comforts (1989, 2003-????, Nick Park)
58. Puss in Boots (1969. Kimio Yabuki)
60. Lupin III (1971-1972, Masaaki Osumi, Hayao Miyazaki & Isao Takahata)
61. Oni (1972, Kihachiro Kawamoto)
62. Gertie the Dinosaur (1914, Windsor McCay)
63. Superman (1941-1943, Dave Fleischer)
64. Jin-Roh. (2000, Hiroyuki Okiura)
65. Once There was a Dog (1982, Eduard Nazarov)
66. House of Flame (1979, Kihachiro Kawamoto)
67. Wallace and Gromit (1989, 1993, 1995, Nick Park)
68. The Cowboy's Flute (1963, Te Wei, Qian Jiajun)
69. Broken Down Film (1985, Osamu Tezuka)
70. Fox and the Hare (1973, Yuri Norstein)
71. Luxo Jr. (1986, John Lasseter)
72. The Nose (1963, Alexandre Alexeieff)
73. The Tale of the White Serpent / Legend of the White Snake (1958, Kazuhiko Okabe, Taiji Yabushita)
73. Allegro non Troppo (1977, Bruno Bozzetto)
75. Royal Space Force: The Wings of Honneamise (1987, Hiroyuki Yamaga)
76. 3000 Leagues in Search of Mother (TV) (1976, Isao Takahata)
77. Tales of a Street Corner (1962, Eiichi Yamamoto, Yusaku Sakamoto)
78. A Grand Day Out (1989, Nick Park)
79. Bad Luck Blackie (1949, Tex Avery)
80. Anne of Green Gables (TV) (1979. Isao Takahata)
81. Good Night Kids (2000, Yuri Norstein, TV)
81. Patlabor 2: The Movie (1993, Mamoru Oshii)
81. Breakfast On The Grass (1987, Priit P?rn)
82. Patlabor 2: The Movie (1993. Mamoru Oshii)
84. Night on the Galactic Railroad (1985, Gisabur? Sugii)
85. The Fabulous World of Jules Verne (1958, Karel Zeman)
86. Mickey Mouse (1928-present?, Walt Disney)
87. Coffee Break (1977, Taku Furukawa)
88. Wile E. Coyote and Road Runner (1949-present?, Chuck Jones)
89. Toot Whistle Plunk and Boom (1953, Ward Kimball)
90. Mt. Head (2002, Koji Yamamura)
91. Popeye (1933-1957, Dave Fleischer)
92. The Overcoat (2 parts) (unfinished, Yuri Norstein)
93. Polychrome Fantasy (1935, Norman McLaren)
94. Panda, Go Panda! (1972, Isao Takahata)
95. Alice (1988, Jan ?vankmajer)
96. The Humpbacked Horse (1947/1975, Ivan Ivanov-Vano)
97. Space Battleship Yamato (1977, Toshio Masuda)
98. Urusei Yatsura 2: Beautiful Dreamer (1984, Mamoru Oshii)
99. Mitten (1967, Roman Kachanov)
99. Deputy Droopy (1955, Tex Avery, Michael Lah)
101. The Super Dimension Fortress Macross (TV) (1983. Noboru Ishiguro)
102. Heavy Metal (1981, Gerald Potterton)
103. Cow (1989, Аlexander Petrov)
104. Flower-Fold (1968, Kihachiro Kawamoto)
105. Virile Games (1988, Jan ?vankmajer)
105. A Thousand and One Nights (1969, Eiichi Yamamoto)
105. Harpya (1979, Raoul Servais)
106. Ghost in the Shell (1995. Mamoru Oshii)
107. A Thousand and One Nights (1969. Eiichi Yamamoto)
109. The Metamorphosis of Mr. Samsa (1977, Caroline Leaf)
110. Powers of Ten (1977, Charles Eames, Ray Eames)
110. Revolver (1993, Jonas Odell, Stig Bergqvist, Martti Ekstrand, Lars Ohlson)
110. Neighbours (1952, Norman McLaren)
113. Le petit soldat (1947, Paul Grimault)
114. F?tiche (1934, Ladislas Starewitch)
115. The Hill Farm (1989, Mark Baker)
116. Tango (1981, Zbigniew Rybczynski)
117. A Well-Ordered Restaurant (1991. Tadanari Okamoto)
118. Papillons de nuit (1997, Raoul Servais, Paul Delvaux)
119. Ashita no Joe 2 (Tomorrow's Joe 2) (TV) (1980, Osamu Dezaki)
119. Street Musique (1972, Ryan Larkin)
121. Lupin III: The Secret of Mamo (Soji Yoshikawa)
122. Adieu Galaxy Express 999 (Rintaro)
123. Shijin no Shougai (1974. Kihachiro Kawamoto)
124. Studie (1929-1933, Oskar Fischinger)
125. The Bead Game (1977, Ishu Patel)
126. Who Framed Roger Rabbit (1988, Richard Williams, (Robert Zemeckis))
127. The Mighty River (1993, Fr?d?ric Back)
128. Dumbo (1941, Ben Sharpsteen)
129. Rainbow Squadron Robin (1966. Takeshi Tamiya)
130. Old Czech Legends (1953, Jir? Trnka)
131. Praise be to Small Ills (1973, Tadanari Okamoto)
132. Princess Mononoke (1997. Hayao Miyazaki)
133. Asparagus (1979, Susan Pitt)
134. Al? Bab? (1970, Giulio Giannini, Emanuele Luzzati) (?)
135. Walking (1969, Ryan Larkin)
136. 8 Man (1963. Haruyuki Kawajima)
137. Canon (1964, Norman McLaren)
138. Porco Rosso (1992. Hayao Miyazaki)
139. Au Fou! (1968, Yoji Kuri)
140. Jabberwocky (1971, Jan ?vankmajer)
141. SPACY (1981, Takashi Ito)
142. The Angel (1982, Patrick Bokanowski)
143. Frog With Guts! (1974, Eiji Okabe, Tadao Nagahama)
144. The Big Snit (1985, Richard Condie)
145. Magical Maestro (1952, Tex Avery)
146. MEMORIES (1995. Morimoto Koji, Okamura Tensai, Otomo Katsuhiro)
147. The Mochimochi Tree (1972, Tadanari Okamoto)
148. ヤクルト「ミルミル」CM / ???? (????, PMBB)
149. Peter Gabriel's "Sledgehammer" (1986, Brothers Quay, others)
150. Bonifas' Holidays (1965, Fyodor Khitruk)
There are some anomalies (Heavy Metal!?) but otherwise it's good stuff.
1. Hedgehog in the Fog (1975, Yuri Norstein)
2. Tale of Tales (1979, Yuri Norstein)
3. Fantasia (1940, Ben Sharpsteen, Hamilton Luske)
4. The Man who Planted Trees (1987, Fr?d?ric Back)
5. The Shepherdess and the Chimneysweep (1952, Paul Grimault)
6. Future Boy Conan (Hayao Miyazaki)
7. My Neighbor Totoro (1988, Hayao Miyazaki)
8. Snow White and the Seven Dwarfs (1937, David Hand)
9. Yellow Submarine (1968, George Dunning)
10. Prince Wanpaku Slays the Great Serpent (1963, Yugo Serikawa)
11. Little Norse Prince (1968, Isao Takahata)
12. Crac (1981, Fr?d?ric Back)
13. Mr. Bug Goes to Town (1941, Dave Fleischer)
14. Wallace & Gromit in The Wrong Trousers (1993, Nick Park)
15. Spider and Tulip (1943, Kenz? Masaoka)
16. Nausicaa of the Valley of the Wind (1984, Hayao Miyazaki)
17. The Snow Queen (1957, Lev Atamanov)
18. Blinkity Blank (1955, Norman McLaren)
19. Laputa Castle in the Sky (1986, Hayao Miyazaki)
20. The Castle of Cagliostro (1979, Hayao Miyazaki)
21. Dimensions of Dialogue (1982, Jan Svankmajer)
22. The Hand (1965, Jir? Trnka)
23. A Midsummer Night's Dream (1959, Jir? Trnka)
24. Night on the Bare Mountain (1933, Alexander Alexeieff & Claire Parker)
25. Dojoji Temple (1976, Kihachiro Kawamoto)
26. The Nightmare Before Christmas (1993, Tim Burton)
27. Fantastic Planet (1973, Ren? Laloux)
28. The Magic Fox (1982, Okon Joruri)
29. Spirited Away (2001 Hayao Miyazaki)
30. AKIRA (1988 Katsuhiro Otomo)
31. Adventures of Ganba (1975. Osamu Dezaki)
31. Tom and Jerry (1965-1972, Joseph Barbera, William Hanna)
33. Astro Boy (TV) (1966 . Osamu Tezuka)
34. Father and Daughter (2000, Michael Dudok de Wit)
35. Pinocchio (1940, Hamilton Luske, Ben Sharpsteen)
36. Mobile Suit Gundam (TV) (1979. Yoshiyuki Tomino)
37. Bambi (1942, David Hand)
38. Street of Crocodiles (1986, Stephen Quay, Timothy Quay)
39. Grave of the Fireflies (1988, Isao Takahata)
40. Betty Boop (1930-1939, Max Fleischer)
41. The Iron Giant (1999, Brad Bird)
42. Cheburashka (1971, Roman Kachanov)
43. Bajaja (1950, Jir? Trnka)
44. The Sand Castle (1977, Co Hoedeman)
45. The Old Man and the Sea (1999, Alexander Petrov)
45. Toy Story (1995, John Lasseter)
45. The Old Mill (1937, Wilfred Jackson) (from the "Silly Symphonies" series)
48. Neon Genesis Evangelion (1995-1996, Hideaki Anno)
48. The Street (1976, Caroline Leaf)
48. The Snowman (1982, Diane Jackson)
51. Jumping (1984, Osamu Tezuka)
52. Heron and Crane (1974, Yuri Norstein)
53. The Emperor's Nightinggale (1949, Jir? Trnka)
54. Monsters, Inc. (2001, Pete Docter)
55. When the Day Breaks (1999, Wendy Tilby, Amanda Forbis)
56. Heidi, Girl of the Alps (TV) (1974. Isao Takahata)
57. Inspirace (1948, Karel Zeman)
58. Creature Comforts (1989, 2003-????, Nick Park)
58. Puss in Boots (1969. Kimio Yabuki)
60. Lupin III (1971-1972, Masaaki Osumi, Hayao Miyazaki & Isao Takahata)
61. Oni (1972, Kihachiro Kawamoto)
62. Gertie the Dinosaur (1914, Windsor McCay)
63. Superman (1941-1943, Dave Fleischer)
64. Jin-Roh. (2000, Hiroyuki Okiura)
65. Once There was a Dog (1982, Eduard Nazarov)
66. House of Flame (1979, Kihachiro Kawamoto)
67. Wallace and Gromit (1989, 1993, 1995, Nick Park)
68. The Cowboy's Flute (1963, Te Wei, Qian Jiajun)
69. Broken Down Film (1985, Osamu Tezuka)
70. Fox and the Hare (1973, Yuri Norstein)
71. Luxo Jr. (1986, John Lasseter)
72. The Nose (1963, Alexandre Alexeieff)
73. The Tale of the White Serpent / Legend of the White Snake (1958, Kazuhiko Okabe, Taiji Yabushita)
73. Allegro non Troppo (1977, Bruno Bozzetto)
75. Royal Space Force: The Wings of Honneamise (1987, Hiroyuki Yamaga)
76. 3000 Leagues in Search of Mother (TV) (1976, Isao Takahata)
77. Tales of a Street Corner (1962, Eiichi Yamamoto, Yusaku Sakamoto)
78. A Grand Day Out (1989, Nick Park)
79. Bad Luck Blackie (1949, Tex Avery)
80. Anne of Green Gables (TV) (1979. Isao Takahata)
81. Good Night Kids (2000, Yuri Norstein, TV)
81. Patlabor 2: The Movie (1993, Mamoru Oshii)
81. Breakfast On The Grass (1987, Priit P?rn)
82. Patlabor 2: The Movie (1993. Mamoru Oshii)
84. Night on the Galactic Railroad (1985, Gisabur? Sugii)
85. The Fabulous World of Jules Verne (1958, Karel Zeman)
86. Mickey Mouse (1928-present?, Walt Disney)
87. Coffee Break (1977, Taku Furukawa)
88. Wile E. Coyote and Road Runner (1949-present?, Chuck Jones)
89. Toot Whistle Plunk and Boom (1953, Ward Kimball)
90. Mt. Head (2002, Koji Yamamura)
91. Popeye (1933-1957, Dave Fleischer)
92. The Overcoat (2 parts) (unfinished, Yuri Norstein)
93. Polychrome Fantasy (1935, Norman McLaren)
94. Panda, Go Panda! (1972, Isao Takahata)
95. Alice (1988, Jan ?vankmajer)
96. The Humpbacked Horse (1947/1975, Ivan Ivanov-Vano)
97. Space Battleship Yamato (1977, Toshio Masuda)
98. Urusei Yatsura 2: Beautiful Dreamer (1984, Mamoru Oshii)
99. Mitten (1967, Roman Kachanov)
99. Deputy Droopy (1955, Tex Avery, Michael Lah)
101. The Super Dimension Fortress Macross (TV) (1983. Noboru Ishiguro)
102. Heavy Metal (1981, Gerald Potterton)
103. Cow (1989, Аlexander Petrov)
104. Flower-Fold (1968, Kihachiro Kawamoto)
105. Virile Games (1988, Jan ?vankmajer)
105. A Thousand and One Nights (1969, Eiichi Yamamoto)
105. Harpya (1979, Raoul Servais)
106. Ghost in the Shell (1995. Mamoru Oshii)
107. A Thousand and One Nights (1969. Eiichi Yamamoto)
109. The Metamorphosis of Mr. Samsa (1977, Caroline Leaf)
110. Powers of Ten (1977, Charles Eames, Ray Eames)
110. Revolver (1993, Jonas Odell, Stig Bergqvist, Martti Ekstrand, Lars Ohlson)
110. Neighbours (1952, Norman McLaren)
113. Le petit soldat (1947, Paul Grimault)
114. F?tiche (1934, Ladislas Starewitch)
115. The Hill Farm (1989, Mark Baker)
116. Tango (1981, Zbigniew Rybczynski)
117. A Well-Ordered Restaurant (1991. Tadanari Okamoto)
118. Papillons de nuit (1997, Raoul Servais, Paul Delvaux)
119. Ashita no Joe 2 (Tomorrow's Joe 2) (TV) (1980, Osamu Dezaki)
119. Street Musique (1972, Ryan Larkin)
121. Lupin III: The Secret of Mamo (Soji Yoshikawa)
122. Adieu Galaxy Express 999 (Rintaro)
123. Shijin no Shougai (1974. Kihachiro Kawamoto)
124. Studie (1929-1933, Oskar Fischinger)
125. The Bead Game (1977, Ishu Patel)
126. Who Framed Roger Rabbit (1988, Richard Williams, (Robert Zemeckis))
127. The Mighty River (1993, Fr?d?ric Back)
128. Dumbo (1941, Ben Sharpsteen)
129. Rainbow Squadron Robin (1966. Takeshi Tamiya)
130. Old Czech Legends (1953, Jir? Trnka)
131. Praise be to Small Ills (1973, Tadanari Okamoto)
132. Princess Mononoke (1997. Hayao Miyazaki)
133. Asparagus (1979, Susan Pitt)
134. Al? Bab? (1970, Giulio Giannini, Emanuele Luzzati) (?)
135. Walking (1969, Ryan Larkin)
136. 8 Man (1963. Haruyuki Kawajima)
137. Canon (1964, Norman McLaren)
138. Porco Rosso (1992. Hayao Miyazaki)
139. Au Fou! (1968, Yoji Kuri)
140. Jabberwocky (1971, Jan ?vankmajer)
141. SPACY (1981, Takashi Ito)
142. The Angel (1982, Patrick Bokanowski)
143. Frog With Guts! (1974, Eiji Okabe, Tadao Nagahama)
144. The Big Snit (1985, Richard Condie)
145. Magical Maestro (1952, Tex Avery)
146. MEMORIES (1995. Morimoto Koji, Okamura Tensai, Otomo Katsuhiro)
147. The Mochimochi Tree (1972, Tadanari Okamoto)
148. ヤクルト「ミルミル」CM / ???? (????, PMBB)
149. Peter Gabriel's "Sledgehammer" (1986, Brothers Quay, others)
150. Bonifas' Holidays (1965, Fyodor Khitruk)
There are some anomalies (Heavy Metal!?) but otherwise it's good stuff.