Two things that REALLY help with pencil drawings are fixative spray and a draftsmans's duster. You see, pencil ALWAYS smears, even if you can't see it. Just the act moving your hand around the paper, unless you lift it completely off will put a fine layer of lead all around the artwork, reducing the contrast. You'll never notice while you are doing it because the process is so gradual, but the scanner does. The biggest contributor to this unwanted "lead layer" (I know modern standard pencils use graphite, but I'm old and I'm gonna still say lead) is again your hand when you brush away eraser crumbs. The solution is a cheap brush that looks alot like the small brush you use to sweep dirt into a dust pan. Use only that to remove eraser crumbs. Touch the artwork as little as possible. I also make an "eraser pass" when I am finished involving erasing all large areas that should be just the paper. This helps the contrast pop quite a bit and will demonstrate the inevitable smear I was talking about earlier.
When the work is done, and I do mean
completely done, take it outside along with the spray fixative.
DO NOT use spray fixative inside.
Ever! Once you spray a piece with fixative,
no more changes. You should have a board larger than the art that you can use low-tack tape (sticky enough to hold temporarily, not enough to pull the art apart when you remove it) to tape the back of the artwork to the board. Ensuring the area is well ventilated, take the spray can and shake it up, then point the nozzle above and to the left of the art. You want to get the flow from the can smoothed out before you point it at your work. Sometimes if a can is new or has not been used in awhile it can spit when you first press the nozzle. Now, like I said, starting above and left of the art, start spraying. At the same time, assuming no spitting or other can malfunction, move your hand in a steady sweeping motion from left to right, holding the nozzle down in the same place. Do not stop moving until you have evenly coated the art top to bottom. any pause or stop will cause more fixative in one place than the rest, and it will be noticeable. Once finished, allow at least fifteeen minutes for the fixative to dry, but I recommend an hour. The matte fixative below will significantly reduce the glare from the lead on the paper. Scanners use reflected light to gather the image, and lead is very reflective. This also prevents smearing from subsequent handling.
You can also set your scanner to increase the contrast of the initial scan.
Lots of links to Dick Blick Art here. No, I do not work for them. They are however the Amazon of art supplies. I have not found cheaper!
Draftsman's Duster
http://www.dickblick.com/products/draftsman-duster/
Spray fixative
http://www.dickblick.com/products/winso ... ive-spray/
Sketch Board - Get the big one and use it only for applying fixative. It will get "gunky" pretty quick.
http://www.dickblick.com/products/blick ... ad-boards/
Low tack tape
http://www.dickblick.com/products/3m-sc ... tist-tape/