Well, it might be shameless, but the credits file included with
Indivisible has basically all the software I used, where to get it, and what I used it for.
Aseprite (Nearly all animation, tileset planning, some promotional material editing) -
http://www.aseprite.org/Pyxel Edit (Ensuring tile counts/Tileset finalization) -
http://pyxeledit.com/NES Screen Tool (Metasprite layouts) -
https://shiru.untergrund.net/software.shtmlYY-CHR (Conversion of some of my graphics to the format NES understands) -
http://www.geocities.jp/yy_6502/yychr/Custom stuff: Two tools to remove duplicate tiles and prepare sprite data made in NES Screen Tool for the extreme bank swapping Indivisible does, and one tool that will take a (possibly animated) image, check it for background errors and create a tileset compatible with bankswapping animation, a metatileset, and a tilemap to be used with Tiled so levels can be built with 16x16 parts.
Pyxel Edit lacking easy tile copying really harms it... I share this image a lot:
http://i.imgur.com/qigHvaN.gifBut it also doesn't really allow one to work with palettized images. I'm working on a small replacement of it for my workflow.
Even without those things it still beats everything for a tile-based workflow, but I always get a little sad that it's really close to being way better than it is...
Edit: Though I really, really don't like it, it's worth looking at
Pro Motion. If you can get used to its UI, it is very powerful, and also allows tilemap editing.
And for good measure, one obscure program which fixes some of Pyxel Edit's tile problems, but I still end up preferring Pyxel Edit:
https://forums.tigsource.com/index.php?topic=14983.0