I had written up my list of top 50 animated movies in January 2013, now, 18 months later, I think I may have watched more animation than over the 24 years before, so I accumulated a large enough number of animated films watched to make a top 100.
After my quick write-up of my favorite top 100 live action films (which are all taken from my previous top 200 for sake of organization) I will write up this list of top 100 animated feature length films (which also includes a couple of shorts between 20 and 45 minutes in length but 90% of the list consists of feature length movies over an hour in length). Given the fact that most adult animated films exists as direct to video movies several of the movies listed here were never released in theaters (although some direct to video movies were later released on theaters or received limited theatrical release). It's very rare to see a list of top 100 cartoon movies mainly because of the limited number of cartoon movies in existence, however, after watching many movies from North America, Europe and Asia (specially Asia, of course, as most of the animated films in the world are made there, more specifically in that little mountainous island near Korea), I was able to list 100 cartoon movies that I liked enough to want to re-watch. The ordering works as follows: 100th place is certainly less preferred than 25th place, however, the 26th place is about as good as the 25th one.
Also notice how recent most entries are (specially if compared to my top 100 live action films list). That's because adult oriented animation began to be produced in large quantities after Nausicaa (1984) and in quantities that are continuously increasing: in 2006 Japan released in theaters more adult animated films than existed in the world up to 1980.
Let's begin:
100. How to Train your Dragon (2009)

Dreamworks finest film, this American fantasy adventure comedy film possesses a charm and an entertainment value equaled by very few movies. The dragon designs are also very interesting and I loved the comedic elements here more than in other Dreamwork films.
99. Jin-Roh: The Wolf Brigade (1999)

A very serious and violent film, depicting an alternate reality were Japan becomes an occupied police state. It's drama can be very powerful and reminds me of samurai films in some ways (the armor the characters wear also is very similar in design to samurai armor). Perhaps Hiroyuki Okiura finest film, though he only directed 2.
98. Steins;Gate the Movie: Loading Area of Déjà vu (2013)

Based on the TV series, this is a powerful drama film (I think I will use those words repetitively in this thread, sorry for my poor writing skills) that also makes numerous (mostly comedic) references to contemporary Japanese otaku culture.
97. Cat Soup (2001)

This Japanese experimental 34 minutes film features a rich surreal imagery and despite it's short run time it possesses more depth than most 2 hour long films.
96. The Triplets of Belleville (2003)

Another weird film makes the list, this time a Chomet film. Despite not being characterized by any explicit fantasy elements, this film is nearly as surrealistic as Cat Soup while possessing a very distinct french sense of style and visuals, very different from Japanese or American animation style.
95. Perfect Blue (1997)

Satoshi Kon's thriller film constitutes one of the very few animated feature length films that make me actually tense and thrilled. Kon was a master of his craft and his early death will be mourned by animation fans all over the world (although he wasn't extremely popular in Japan).
94. Strike Witches: The Movie (2012)

My guilty pleasure, this is one of the standards of the emerging military moe genre. Despite featuring a combination of extremely ludicrous elements (such as pantless teenager girls which grows tails and cat ears when they use their magic powers, yes, this is perverted stuff, among the worst examples in animation) it is essentially a typical action drama film in terms of writing and direction, nothing special in those regards besides it's more Japanese sensibilities.
93. Angel's Egg (1985)

Another animated art film (perhaps to compensate for the movie above
) this is the first Mamoru Oshii film on this list and indeed an impressive work of art. Perhaps the only example of animation that I watched that fells like super serious symbolic art cinema.
92. Cowboy Bebop: The Movie (2001)

According to film critic Noel Vera, this was the coolest film of the year released in the Philippines in 2003. Indeed, the single word "cool" could be a review of this film which feels very much like the original TV series (as if it were a very long episode of the TV series).
91. Voices of a Distant Star (2003)

This Makoto Shinkai half an hour short is the first of his works to show up on this list and it's easy to see why: Shinkai is a master of the use of still watercolor images to depict the feelings of it's characters.
After my quick write-up of my favorite top 100 live action films (which are all taken from my previous top 200 for sake of organization) I will write up this list of top 100 animated feature length films (which also includes a couple of shorts between 20 and 45 minutes in length but 90% of the list consists of feature length movies over an hour in length). Given the fact that most adult animated films exists as direct to video movies several of the movies listed here were never released in theaters (although some direct to video movies were later released on theaters or received limited theatrical release). It's very rare to see a list of top 100 cartoon movies mainly because of the limited number of cartoon movies in existence, however, after watching many movies from North America, Europe and Asia (specially Asia, of course, as most of the animated films in the world are made there, more specifically in that little mountainous island near Korea), I was able to list 100 cartoon movies that I liked enough to want to re-watch. The ordering works as follows: 100th place is certainly less preferred than 25th place, however, the 26th place is about as good as the 25th one.
Also notice how recent most entries are (specially if compared to my top 100 live action films list). That's because adult oriented animation began to be produced in large quantities after Nausicaa (1984) and in quantities that are continuously increasing: in 2006 Japan released in theaters more adult animated films than existed in the world up to 1980.
Let's begin:
100. How to Train your Dragon (2009)

Dreamworks finest film, this American fantasy adventure comedy film possesses a charm and an entertainment value equaled by very few movies. The dragon designs are also very interesting and I loved the comedic elements here more than in other Dreamwork films.
99. Jin-Roh: The Wolf Brigade (1999)

A very serious and violent film, depicting an alternate reality were Japan becomes an occupied police state. It's drama can be very powerful and reminds me of samurai films in some ways (the armor the characters wear also is very similar in design to samurai armor). Perhaps Hiroyuki Okiura finest film, though he only directed 2.
98. Steins;Gate the Movie: Loading Area of Déjà vu (2013)

Based on the TV series, this is a powerful drama film (I think I will use those words repetitively in this thread, sorry for my poor writing skills) that also makes numerous (mostly comedic) references to contemporary Japanese otaku culture.
97. Cat Soup (2001)

This Japanese experimental 34 minutes film features a rich surreal imagery and despite it's short run time it possesses more depth than most 2 hour long films.
96. The Triplets of Belleville (2003)

Another weird film makes the list, this time a Chomet film. Despite not being characterized by any explicit fantasy elements, this film is nearly as surrealistic as Cat Soup while possessing a very distinct french sense of style and visuals, very different from Japanese or American animation style.
95. Perfect Blue (1997)

Satoshi Kon's thriller film constitutes one of the very few animated feature length films that make me actually tense and thrilled. Kon was a master of his craft and his early death will be mourned by animation fans all over the world (although he wasn't extremely popular in Japan).
94. Strike Witches: The Movie (2012)

My guilty pleasure, this is one of the standards of the emerging military moe genre. Despite featuring a combination of extremely ludicrous elements (such as pantless teenager girls which grows tails and cat ears when they use their magic powers, yes, this is perverted stuff, among the worst examples in animation) it is essentially a typical action drama film in terms of writing and direction, nothing special in those regards besides it's more Japanese sensibilities.
93. Angel's Egg (1985)

Another animated art film (perhaps to compensate for the movie above

92. Cowboy Bebop: The Movie (2001)
According to film critic Noel Vera, this was the coolest film of the year released in the Philippines in 2003. Indeed, the single word "cool" could be a review of this film which feels very much like the original TV series (as if it were a very long episode of the TV series).
91. Voices of a Distant Star (2003)

This Makoto Shinkai half an hour short is the first of his works to show up on this list and it's easy to see why: Shinkai is a master of the use of still watercolor images to depict the feelings of it's characters.