Batch fill the transparent backgound

[Ofnuts]

Are all the sprites the same size and not too big? If so you can load them all as tiles in a single layer, edit the layer, and split them back. Some of my scripts that can help:

• ofn-tiles: loads/save multiple files as one layer and vice-versa
  
• ofn-layer-tiles: split a single layer to tile and vice-versa
  
• ofn-export-layers: exports all your layers to files, using a pattern to name them.
  
• replace-foreground-by-background: replace the background color by the foreground color, usually after you have done a selection on the background (and grown it by one or two pixels, see here why).
  
• ofn-file-next: saves & closes current image and loads next in sequence, usually assigned to a shortcut. Very often this is where you spend the most time when mass-editing images.
  

All scripts here.