I didn't expect this but while making this list I realised that 2006 was a great year for animation. It brought us a huge amount of animated movies for both, kids and adults. Maybe this year didn't have The Movie but it had some iconic movies and also a lot of less known but still great movies and shorts.
Highest-grossing films of 2006:
1) Ice Age: The Meltdown
3) Happy Feet
4) Over the Hedge
5) Open Season
This list also contains some shorts. Movies are in no specific order. Some movies may be missing.