What do you know, Doukutsu (aka Cave Story) can be played with a Gamepad! For a Xbox controller this is how I set the controls:
And how to configure it:
Works great. I love this game. If you don’t want to install Wine (the configuration tool requires Wine) you can download this config file and place it as ‘~/.doukutsu/Config.dat.
tar -xvf doukutsu-config.tar.gz -C ~/
It’s an executable file (probably because the Wine app edited it), haven’t bothered changing it :).