Just found out that GIMP 2.9
recently gained some basic indexpainting support[1]
While the performance of GIMP 2.9 is currently pretty slow while they work through all the different changes needed to make high bitdepth support available in everything, and it'll never provide the degree of control you can get with eg. GrafX2, it's quite pleasing if you just want to do some minor edits.
Support includes (this is basically a list of everything in GIMP that is currently using GEGL):
* Full greyscale selection mask support (ie. you can generate some plasma as your selection mask, and then drop a greyish color on the canvas to layer some fog over the image)
* all 'basic' operations like paste, paste into, fill, pattern fill,
* All drawing modes; and drawing with lowered opacity
* Layer modes and opacity (but you don't get an indexized preview until you do 'new from visible', only a full RGB one.)
* Painting with 'paintbrush' and 'ink' tools (ie. the brush is plotted with levels of opacity, not just binary transparency)
* gradients (heh)
* most color filters, eg curves, levels -- this doesn't modify the palette but the image content. Posterize can be surprisingly useful.
* cage transform tool, smudge tool, clone tool, dodge/burn tool
* transform tool preview opacity works.
[1] The relevant news item is 'High bit depth processing available now'. As I write this, it is the fourth item from the top.