The Pencil Tool (chosen by clicking its icon in the options bar) lets you draw pixels into the current layer. The color drawn by the Pencil Tool is the current primary color. When the Pencil Tool is selected you can change its radius in the options bar.
The Eraser Tool (chosen by clicking its icon in the options bar) lets you erase pixels from the current layer. When the Eraser Tool is selected you can change its radius in the options bar just like with the Pencil Tool. The Eraser Tool works by drawing pixels in the mask of an image, so it can even be used to "erase" pixels from vectors.
The Fill Tool (chosen by clicking its icon in the options bar) lets you fill in pixels in a shape. The color filled is the current primary color. When you click on the canvas, the color will be applied to every pixel that has an original color close enough to that of the pixel you clicked. You can change the sensitivity to color changes in the options bar.