The 2 paint programs I've used the most over the more recent years are TVPaint and FXPaint.
TVPaint was released for free and you can download the latest version
HERE.TVPaint is kick ass on WinUAE as it's 24bit support is great.
Not sure what happened to FXPaint though. I know I got mine through IOSpirite a couple years ago, but looks like they stopped carrying Amiga software??