Pixel art is one thing, but map making is something else on its own (and yet still related). I've worked mostly with photoshop, and find gimp and some other programs to be cumbersome. Although I'm sure that's probably more of a matter of experience with one, and less with the other.
As far as pixel art - whatever you're most comfortable with, usually does the trick. When it comes to tiles, maps, and all things subpalettes - then I would say there's no good application out there for the PCE. This is where home grown tools for the system come into play. I tend to use mappy for maps, when I need something quick - but I have tools that embedded PCE subpalette data right into the pixel values so that I can convert it into proper multiple subpalette tilemap/tileset conversion without having to remap or define it on the compiler/assembler side (I don't use mappy FMP include support; my stuff is raw data at that stage). And even then, it's not really optimal. I have the same set of tools that works back into photoshop - allowing me with work with 16 individual subpalettes directly (tiles or sprites). I might be over looking Promotion, as I only use it for limited/specific stuffs, but it is designed around tile and map functionality (it's directly built in). And there are sprite programs out there specifically designed to aid in the creation of animation.
But if you're going to get that committed, you might as well drop mappy and incchr, and all the libs associated with them - and write your own library handling code. Just my opinion though...