If we're talking about the 90s, it'd be confusing because for most of the decade, there were only about 3 or 4 animated films per year, but i'd choose 1996, for the simple fact that what films were released to theaters (Space Jam, Beavis and Butt-Head Do America, The Huntchback Of Notre Dame) were of very high quality.
The 2000's, on the other hand, expanded the amount of animated films in a year, and if we're talking the 2000's, i'd pick the tail end of the decade, 2009, because the movies that they had showed a professional amount of progression from other films in the decade, of which could only fall behind the 80's as the worst decade for animated films, but whatever, because 2009 had a lot of great films released (Up, The Princess And The Frog, Coraline, Cloudy With A Chance Of Meatballs, etc.) to overshadow the amount of feces that were in that decade.
For the 2010s, erm... 2014? I'm only saying that because in each consecutive year, we seem to have one movie that is so ::dolphin noise::, it ruins my perception of the year. (2010 had that really disappointing Drawn Together movie, 2011 had Hoodwinked Too, a sequel I don't know why was made, 2012 had Foodfight which speaks for itself, 2013 was cluttered with bad films like Free Birds and that DTV Tarzan movie) I can't think of anything for this year, minus Nut Job and that one Oz movie, and while those are bad, they're not excruciating to watch, and I can easily name great movies that the year had, (Big Hero 6, The Lego Movie, The Book of Life) with their quality being amazing.
