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ProDAD Mercalli has batch processing
A few days ago ProDAD introduced Mercalli 4.0 (not released yet). Maybe in this new version they will fix it.
@Vesku
What NLE are you using?
Vegasaur for Sony Vegas Pro can batch stabilize clips, but it does not support Movie Studio versions.
Haven't tried it but this claims to do it:
http://tylerhurd.blogspot.com/2013/01/batch-stabilize-footage.html