Aseprite is a great pixel art tool.
It doesn't support custom formats yet but we'll be able to create plugins in the future (see here).
Anyway, it's open source so I built a version with GRP support myself and it works pretty much perfectly.
This is a Windows version but I included information about the edits I made so anyone can compile for Mac, Linux or improve it.
It supports both raw GRP files (extracted through PetitModem) and dumped ones (from the game's extdata). You need to add the .GRP extension to the filenames, though.
I don't know how to operate the software very well yet so the only way I found to use the transparent color is by going to Layer > Layer from Background before doing anything.
If you don't do that you'll see the transparency but will only be able to paint solid colors even when you pick the transparent one (#000000)
Also remember that the GRP images are always 512x512 pixels big.
Keep this in mind if you plan to convert other images to this format.
EDIT: updated to v1.1.10