Not sure if things have changed so significantly since the question was originally but modern answer using current arduino IDE libraries. Don't assign the EEPROM value to a variable as then you are wasting precious SRAM again. EEPROM has unlimited read cycles. I can't find any current references to EEPROM.read() as a Macro or function in the Arduino IDE.

#include  <avr/eeprom.h>

// the setup routine runs once when you press reset:
void setup() {
/* The "131" value is used to prevent damaging excess EEPROM writes on every restart.
   If you want to try setting a different GPIO pin for LED blink change the test value in
   both the read and following write to EEPROM address 511 */

    if (eeprom_read_byte((uint8_t*)511) != 131) {
       eeprom_write_byte((uint8_t*)511,131);
// Store the GPIO pin number in EEPROM address 1     
       eeprom_write_byte((uint8_t*)1,1); 
    };
// initialize the digital pin as an output.
    pinMode(eeprom_read_byte((uint8_t*)1), OUTPUT); // LED pin value stored in EEPROM address 1
}

// the loop routine runs over and over again forever:

void loop() {
    digitalWrite(eeprom_read_byte((uint8_t*)1), HIGH);
    delay(1000);               // wait for a second
    digitalWrite(eeprom_read_byte((uint8_t*)1), LOW);

    delay(1000);               // wait for a second
}

Not sure if things have changed so significantly since the question was asked originally but I'll answer using the Atmel AVR libraries. 

Don't assign the EEPROM value to a variable as then you are wasting precious SRAM again. EEPROM has unlimited read cycles. 

I can't find any current references to EEPROM.read() as a Macro or function in the Arduino IDE. Instead there is the AVR EEPROM library which uses eeprom_read_byte() as shown below.

#include  <avr/eeprom.h>

// the setup routine runs once when you press reset:
void setup() {
/* The "131" value is used to prevent damaging excess EEPROM writes on every restart.
   If you want to try setting a different GPIO pin for LED blink change the test value in
   both the read and following write to EEPROM address 511 */

    if (eeprom_read_byte((uint8_t*)511) != 131) {
       eeprom_write_byte((uint8_t*)511,131);
// Store the GPIO pin number in EEPROM address 1     
       eeprom_write_byte((uint8_t*)1,1); 
    };
// initialize the digital pin as an output.
    pinMode(eeprom_read_byte((uint8_t*)1), OUTPUT); // LED pin value stored in EEPROM address 1
}

// the loop routine runs over and over again forever:

void loop() {
    digitalWrite(eeprom_read_byte((uint8_t*)1), HIGH);
    delay(1000);               // wait for a second
    digitalWrite(eeprom_read_byte((uint8_t*)1), LOW);

    delay(1000);               // wait for a second
}