For example, most anime drawings only use up to four different shades for one color, probably to speed up the time it takes to draw a cel. Draw an outline first. If you're drawing a person, draw a rough outline of their head, arms, legs, and torso. If you're doing a tree, outline the limbs. This outline won't be permanent, and should be done with a very light pencil that is easy to erase, like a 2H. This usually helps precision problems when drawing, and really helps with the proportions when drawing people.
Scanners usually brighten the image a great deal.
When darkening the image, raise the contrast to keep the lines visible. You can use a freehand or polygonal selection tool to cut out the parts you don't want in your picture. If your picture takes too long to load on the internet, try reducing the number of colors in a GIF, or for JPEG, optimizing it for smaller file size. Although it may result in a loss of quality, usually you can reduce it alot without seeing a difference. I recommend saving the pictures in a JPEG format for the web.