user31494: I have a simple photoresistor displaying values on a serial monitor every second so I can establish a value that I want to use to have it activate a relay.
It has worked fine for a few weeks, with bright sunlight values about 1000, total dark is 0. I soldered only the headers on a protoshield, and stacked it on the Arduino. I have nothing else on the protoshield and I am still using jumper wires to a breadboard, which I have not changed.
Why would the photoresistor values drop to approximately 40 (from 900's) when I stack the second board on the Arduino? 

user30198: It should not happen.
I have changed this answer, because at first I read that the resulting value was changed by -40, but I think it drops from 900 to 40.
The shield is doing something, so it is not empty. Perhaps it shortcuts the AREF to GND. Perhaps you are reading an open input, and the sensor is at another analog pin. Perhaps the shield does something to the voltage pins.
A breadboard can have bad contacts. The shield can have bad contacts.
Be sure that the sensor is connected to the channel that you are reading. Measure the voltage at that analog input with a multimeter with and without the shield. Check the 5V, 3.3V and AREF pins with and without the shield.

user23791: Does the proto-shield have any LEDs on it?
You were probably connected to a pin unknowingly.
How is resistance being measured? A voltage divider with an analogRead()? 
Using a cheapo multimeter can cause problems. 
Possibly, his proto-shield has some trace "wires" etched into it that were unseen, and he was connected to a floating pin or ground. 
Or maybe the shield was shifted over one pin, and he wasn't connected to the pins he thought.

31494: <p>I have a simple photoresistor displaying values on a serial monitor every second so I can establish a value that I want to use to have it activate a relay.</p>

<p>It has worked fine for a few weeks, with bright sunlight values about 1000, total dark is 0. I soldered only the headers on a protoshield, and stacked it on the Arduino. I have nothing else on the protoshield and I am still using jumper wires to a breadboard, which I have not changed.</p>

<p>Why would the photoresistor values drop to approximately 40 (from 900's) when I stack the second board on the Arduino? </p>
 30198: <p>It should not happen.</p>

<p>I have changed this answer, because at first I read that the resulting value was changed by -40, but I think it drops from 900 to 40.</p>

<p>The shield is doing something, so it is not empty. Perhaps it shortcuts the AREF to GND. Perhaps you are reading an open input, and the sensor is at another analog pin. Perhaps the shield does something to the voltage pins.</p>

<p>A breadboard can have bad contacts. The shield can have bad contacts.</p>

<p>Be sure that the sensor is connected to the channel that you are reading. Measure the voltage at that analog input with a multimeter with and without the shield. Check the 5V, 3.3V and AREF pins with and without the shield.</p>
 23791: <p>Does the proto-shield have any LEDs on it?</p>

<p>You were probably connected to a pin unknowingly.</p>

<p>How is resistance being measured? A voltage divider with an <code>analogRead()</code>? 
Using a cheapo multimeter can cause problems. </p>

<p>Possibly, his proto-shield has some trace "wires" etched into it that were unseen, and he was connected to a floating pin or ground. </p>

<p>Or maybe the shield was shifted over one pin, and he wasn't connected to the pins he thought.</p>
