To the best of my knowledge there is no difference in the formatting of the screenplay weather it's live action or animted. I found a screenplay for an anime feature on scriptcrawler called "Star Blazers," follow this link to get to it;
http://www.scriptcrawler.com/scripts.php?script=anime&alpha=s . Scriptcrawler.com has loads of stuff in their anime section but this is the only one I found that wasn't listed as a transcript. Transcripts tend to be bad examples of how to set up a script. They are not the actual screenplay, just some dude who had too much times on their hands' written recording of an existing film.
Anyway "Star Blazers" appears to be a screenplay, not a transcript. I suspect you'll have trouble finding screenplays for anime as they tend to be written in Japanese or something that's not English. I did try putting some titles of animated films in English into a scriptcrawler search but came up negative. Anyway, good luck.
EDIT: Might not be exactly what you're looking for but I just found a link for the "Wall E" screenplay which Disney/Pixar have made available for public download
http://disneystudiosawards.movies.go.com/main.html? 
