He very likely used Cosmigo Pro Motion (78$), which is basically the industry standard for people who make a living of pixel art. Still you should be aware that he probably spent 95% time painting with the single pixel brush or picking a color from the palette.
What matters is that you can use a program where you're comfortable zooming, scrolling, drawing, picking colors. Keyboard shortcuts (and mouse wheel etc.) are very important if you don't want to waste time moving your mouse from the drawing area to toolbars and back.
I'm the current coder of Grafx2 and I can confirm it's one of the right tools for such game graphics.

By the way, you may want to also check Mrmo Tarius's works, he has improved tremendously in the last year and I find his way of mixing colors similar to Helm's and Ptoing's. Mrmo's pieces being smaller and simpler, you may find them easier to study and learn from.