obviously you want to convert jpgs to cmap images. the question is why do this in windows? wouldn't making an amiga anim be easier with an amiga? even using WinUAE?
I use ACDSee to view iff's (and everything else) in windows, but i've never used it to convert to iff. i suppose it could. with plugins Photoshop and AfterEffects also load and save iff's.