Hey Corinne –
The animation was entirely hand-made in the main title sequence for Juno. I know this because I was one of the two designers who patiently worked on it for months! We didn’t use any Photoshop filters – just a good set of color pencils, pens and scissors. After Effects was used to composite the background drawings and the hand cut-outs of Juno.
For more info, check out our making-of Flickr gallery:
https://flickr.com/photos/shadowplaystudio/sets/72157603777361412/
And here’s an article that goes over the process in a bit more detail:
https://mmbase.submarinechannel.com/titlesequences/video.jsp?video=30075
Hope this helps,
– g