That all said, you can do everything necessary to make a tileset in GIMP, and the actual drawing process is just as easy as in any other program (in my opinion, anyway). Just observe all the usual conditions for JJ2 tilesets.

If you can't figure out how to make your image a 256 color bitmap, you need to change the image mode to indexed; in GIMP, use Colors -> Mode -> Indexed. Make your palette first, unless the tileset already has the exact colors you want in the palette, including the JJ2 sprite colors, and no others. (You will still have to rearrange them with the Rearrange Colormap option, unless you make an especially bizarre tileset where all the colors occur in the same order they are in the palette. You can do this by placing a previously made palette in the image as the first 256 pixels along the top row, if for some reason you want to.)

GIMP allows you to create and edit palettes, but it's very clunky; you can't even change multiple colors at once. While it's possible to create an entire, perfect JJ2 palette this way, you're better off using an external program like PalSuite or TilesetPal.

Do not try to use the Set Colormap option to change the palette of your tileset, because it doesn't remap the pixel's indexes - you'll get a "palette swap" effect. For a rather contrived example, if you had a palette of two colors, black and white, and another palette of two colors, white and black, using Set Colormap to switch the two would cause black to become white and white to become black.
Set Colormap is useful if you've edited an existing tileset's palette externally and want to apply it to the tileset, for fairly obvious reasons.

Another caution about palettes in GIMP: faced with two or more identical colors in the palette, it will ALWAYS use the first one if you are drawing in the tileset or adding/converting palettes with the Indexed... dialog. Yes, even if you use the Color Pick function to choose the second one, it will draw as the first one. However, changing the palette and only the palette will allow you to use the second (or third or whatever) color; change the duplicate color to a unique color in the palette, draw with that unique color, then change it back in the palette.

(And yes, duplicate colors are sometimes useful in JJ2 tilesets. Sort of.)