i'd say nope. but a request for adding support into ffmpeg - with no reply of course:
http://www.mail-archive.com/ffmpeg-i.../msg00855.html
there is ProMotion (
http://www.cosmigo.com/promotion/index.php ) which can open ANIMs, but not save (just tested the demo version) - not sure, if full version can export them.
Using winuae and Convert2CDXL is a possibility:
http://www.cd32-allianz.de/cdxl/convert2cdxl/intro