The Paintbrush tool is the default tool when starting Paint.NET. It gives you the ability to draw freeform on your document using a mouse or a stylus. The value of Brush Width will determine how many pixels wide your brush will be.
Note
When you use the Brush tool, left-clicking will paint over the image with the primary color you've chosen from the color wheel. Right-clicking will paint over your image with the secondary color you have chosen.
Eraser (shortcut key E)
The Eraser tool will erase any part of the image you use it on, making it transparent.
This is good for erasing some backgrounds, but not as ideal as using the Magic Wand. The Eraser tool can be refined with its own Brush tool and Antialiasing.
Note
The checkered background you see when you erase part of a picture will not show up in your image. It is there to show transparent areas in your image.
Pencil (shortcut key P)
The Pencil tool allows you to draw one pixel at a time.
You can get almost the same result using the Paint Brush tool with a brush width of 1px and the Antialiasing disabled.