Just a quick specific one:  It has been documented that, when someone
is deprived of light for an extensive period of time (i.e. prisoner
confined in a dungeon, mule working in a coal mine, etc.), they
eventually go blind.  Where, specifically does the atrophy occur? 
(retina?  optic nerve?  visual cortex in the brain?)

Thank you for accepting my findings as your answer. I've reposted the
material below, with two additional links that I think you'll find
interesting.

"Dan Feldman, an assistant professor of biology from the University of
California at San Diego, comments the experiments by Bear and
colleagues 'have proven, quite nicely, that sensory deprivation
induces the form of synaptic weakening called LTD and that the process
actually happens in the visual cortex. Generally, this finding helps
us understand how the brain stores information about experience. And
specifically, for kids who have occluded vision in one eye, we now
understand why that eye's input gets disconnected from the visual
cortex,' Feldman says."

Healthfinder
http://www.healthfinder.gov/news/newsstory.asp?docID=514321

"The years between birth and age seven are critical to visual
development in children. Visual sensory deprivation during this time
can lead to blindness in one or both eyes, says Associate Professor of
Ophthalmology Scott Lambert."

Emory University
http://www.emory.edu/EMORY_MAGAZINE/fall95/health.html

"Cortical plasticity persists after age 20. This is consistent with an
extensive literature documenting instances where sensory deprivation
altered cortical functions in adult animals and humans."

Journal of Neurophysiology
http://jn.physiology.org/cgi/content/full/88/6/3359

"Sensory experience during development can profoundly affect brain
function. For instance, undergoing a period of visual deprivation in
one eye shortly after birth leads to blindness in that eye because
neurons in the visual cortex of the brain lose the ability to respond
to stimuli... This loss does not result simply from reduced neuronal
activity, but depends on residual activity from the deprived retina.
The underlying mechanisms, however, remain unclear."

Science Magazine
http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2003/194/tw300

"Torsten Wiesel and I took a kitten a week old, when the eyes were
just about to open, and sewed shut the lids of one eye. The procedure
sounds harsh, but it was done under anesthesia and the kitten showed
no signs of discomfort or distress when it woke up, back with its
mother and litter-mates. After ten weeks we reopened the eye
surgically, again under an anesthetic, and recorded from the kitten's
cortex to learn whether the eye closure had had any effect on the eye
or on the visual path....

The results of the kitten experiment amazed us. All too often, an
experiment gives wishy-washy results, too good to dismiss completely
but too indecisive to let us conclude anything useful. This experiment
was an exception; the results were clear and dramatic. When we opened
the lids of the kitten's eye, the eye itself seemed perfectly normal:
the pupil even contracted normally when we shined a light into it.
Recordings from the cortex, however, were anything but normal.
Although we found many cells with perfectly normal responses to
oriented lines and movement, we also found that instead of about half
of the cells preferring one eye and half preferring the other, none of
the twenty-five cells we recorded could be influenced from the eye
that had been closed."

Department of Neurology, Harvard Medical School
http://neuro.med.harvard.edu/site/dh/b50.htm
 
Google Web Search: "sensory deprivation" + "blindness"
://www.google.com/search?hl=en&ie=UTF-8&oe=UTF-8&q=%22sensory+deprivation%22+blindness

Google Web Search: "deprivation" + "cortical blindness"
://www.google.com/search?hl=en&ie=UTF-8&oe=UTF-8&q=%22deprivation+%22cortical+blindness

I hope this information will be useful. If anything is unclear, or if
a link does not function, please request clarification; I'll be glad
to offer further assistance before you rate my answer.

Best regards,
pinkfreud

Thanks, all of you, for some great info!

I'm not sure how much detail you need, but I've found several links
that may be of use:

"Dan Feldman, an assistant professor of biology from the University of
California at San Diego, comments the experiments by Bear and
colleagues 'have proven, quite nicely, that sensory deprivation
induces the form of synaptic weakening called LTD and that the process
actually happens in the visual cortex. Generally, this finding helps
us understand how the brain stores information about experience. And
specifically, for kids who have occluded vision in one eye, we now
understand why that eye's input gets disconnected from the visual
cortex,' Feldman says."

http://www.healthfinder.gov/news/newsstory.asp?docID=514321

(The entire article linked above may be of interest to you.)

"The years between birth and age seven are critical to visual
development in children. Visual sensory deprivation during this time
can lead to blindness in one or both eyes, says Associate Professor of
Ophthalmology Scott Lambert."

http://www.emory.edu/EMORY_MAGAZINE/fall95/health.html

"Cortical plasticity persists after age 20. This is consistent with an
extensive literature documenting instances where sensory deprivation
altered cortical functions in adult animals and humans."

http://jn.physiology.org/cgi/content/full/88/6/3359

If this material is fully satisfactory, I'll be glad to repost it as
the answer to your question.

"Specifically" it occurs in the cortex of the brain, mostly at the
primary visual cortex, but also at "higher" visual areas that process
visual stimuli (V2, V3, V4, area MT, etc)  The neurons that would
generally be processing visual stimuli, if no longer receiving input,
can be "taken over" by other areas to perform other functions.  This
phenomenon is called "cortical plasticity"; it does not happen in the
other areas you mentioned, such as the optic nerve nor retina
(different types of neurons, and no competing neurons to overtake
them, lots of other reasons too)

To clarify some of pinkfreud's material (which seems quite good; would
certainly be reasonable and worth $3 to have her post it as an answer)
this cortical rearrangement of neuronal function indeed can occur in
adults.  However, neurons during development are much more susceptible
to this type of plasticity.

Anyway, enough for now...
-Andrewxmp

yes - thanks a bunch you two.  Go ahead and post it as an answer.

I did a bit of research on this as well and agree with my colleagues. 
Here are a few links that I hope will prove useful.

Long-term deprivation affects visual perception and cortex.
Fine I, Wade AR, Brewer AA, May MG, Goodman DF, Boynton GM, Wandell BA, MacLeod DI.
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=npg&cmd=Retrieve&db=PubMed&list_uids=12937420&dopt=Abstract

Eye and Its Parts (diagram)
http://www.99main.com/~charlief/Blindness.htm

I'm not certain how far you want to get into this but you might want
to check this source:

Grassian S and Friedman N, Effects of Sensory Deprivation in
Psychiatric Seclusion and Solitary Confinement, International Journal
of Law and Psychiatry, 8:49-65, 1986.

And the prison at Port Arthur, Tasmania, might make for an interesting subject.

"It was interesting for the author to note that beside the prison at
Port Arthur, Tasmania, a psychiatric asylum was built to literally
connect to the prison proper. This was in view of the large proportion
of inmates who developed psychosis in the course of their extended
periods of internment, requiring transfer. The prison boasted an
ideology that the prisoners would benefit from a process of spiritual
cleansing which would be obtained by sensorially depriving them of all
input other than a bible in their cell and weekly sermons. They were
allowed out of their cells one-hour per day, to walk in a designated
area without social contact."
http://members.optushome.com.au/drgg/gg/sensory.htm 
http://www.portarthur.org.au

Best of luck on your project,
V

Thank you for the five-star rating and the tip!

~pinkfreud