Designing Custom Graphics

use paint.net or photo shop.

For retro pixel art style graphic I'm suggesting you to use Aseprite it makes drawing connecting textures for blocks like cobblestone easier and you don't have to be very careful with arranging them also it has some useful features like resizing pictures by 2 so that your texture is not streached in any way

For items I'm suggesting to draw for example swords in 32x32 but one square is 4 pixels it makes it look somehow better, note draw it like in 16x16 but on 32x32 canvas 

there even asprite or  even gimp 

I recommend using GIMP, it's really simple to learn and I've never had to watch more than 30 seconds of a tutorial to find out how to do something with it. Very versatile, it's how I make all my item and block textures - see my mods.