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(5 edits)

I use GameMaker Studio and Photoshop mainly, but when doing more detailed 2D animation I use Plastic Animation Paper, which is great for pencil- or ink-style animation (bonus: it's free).

I also have this neat tool called Autostitch, for making panoramas out of photos. Not something I use for games often right now, but pretty handy if you ever need to do a skybox.