user29824: I know this is a problem that has come up many times but I can't seem to get this code fragment to update the count variable on an ATMEGA328P. I am using an Arduino Uno as a development board, with the LED on pin 13 set to flash for debugging. I have confirmed the timer and LED part work by toggling port B pin 5 in the ISR routine.
#include <avr/io.h>
#include <avr/interrupt.h>

volatile uint8_t count;

void init_100us_tick(void) {
    TCCR0A = _BV(WGM01) | _BV(WGM00);       // WGM mode 7 with OCRA as top
    TCCR0B = _BV(WGM02) | _BV(CS01);        // CLK / 8 prescaler
    TIMSK0 = _BV(OCIE0B) | _BV(TOIE0);      // Interrupt enabled on OCR0A
    OCR0A = 200;                            // 16 MHz / 8 / 200 = 100 us
    sei();                                  // Enable interrupts
}

ISR(TIMER0_COMPB_vect) {
    count++;
}

int main(void) {
    DDRB |= _BV(DDB5);                      // PB5 output
    init_100us_tick();                      // Initialise 100 us tick
    count = 0;                              // In case of micro reset

    for (;;) {
        if (count >= 100) {                 // Every 10 ms
            count = 0;
            PORTB ^= _BV(DDB5);             // Toggle PB5
        }
   }
   return 0;
}

This is being compiled and burned to an Arduino Uno with the following:
avr-gcc -Os -DF_CPU=16000000UL -mmcu=atmega328p -c -o test.o test.c
avr-gcc -mmcu=atmega328p test.o -o test
avr-objcopy -O ihex -R .eeprom test test.hex
avrdude -F -V -c arduino -p ATMEGA328P -P /dev/ttyUSB0 -b 115200 -U flash:w:test.hex

I have tried disabling the optimisation with no effect. AVR-GCC is version 4.9.2

user10794: You want CTC mode for that to work. As in:
#include <avr/io.h>
#include <avr/interrupt.h>

volatile uint8_t count;

void init_100us_tick(void) {
    TCCR0A = _BV(WGM01);       // CTC mode 2 with OCRA as top
    TCCR0B = _BV(CS01);        // CLK / 8 prescaler
    TIMSK0 = _BV(OCIE0B) | _BV(TOIE0);      // Interrupt enabled on OCR0B
    OCR0A = 200;                            // 16 MHz / 8 / 200 = 100 us
    sei();                                  // Enable interrupts
}

ISR(TIMER0_COMPB_vect) {
    count++;
}

int main(void) {
    DDRB |= _BV(DDB5);                      // PB5 output
    init_100us_tick();                      // Initialise 100 us tick
    count = 0;                              // In case of micro reset

    for (;;) {
        if (count >= 100) {                 // Every 10 ms
            count = 0;
            PORTB ^= _BV(PORTB5);             // Toggle PB5
        }
   }
   return 0;
}

That toggles every 10 ms.

(Edited to add)
The PWM mode you chose will work providing you enable the correct interrupt. This also outputs 10 ms pulses:
#include <avr/io.h>
#include <avr/interrupt.h>

volatile uint8_t count;

void init_100us_tick(void) {
    TCCR0A = _BV(WGM01) | _BV(WGM00);       // Fast PWM mode 7 with OCRA as top
    TCCR0B = _BV(WGM02) | _BV(CS01);        // CLK / 8 prescaler
    TIMSK0 = _BV(OCIE0A);                   // Interrupt enabled on OCR0A  ***
    OCR0A = 200;                            // 16 MHz / 8 / 200 = 100 us
    sei();                                  // Enable interrupts
}

ISR(TIMER0_COMPA_vect) {                    // Compare A vector ***
    count++;
}

int main(void) {
    DDRB |= _BV(DDB5);                      // PB5 output
    init_100us_tick();                      // Initialise 100 us tick
    count = 0;                              // In case of micro reset

    for (;;) {
        if (count >= 100) {                 // Every 10 ms
            count = 0;
            PORTB ^= _BV(PORTB5);           // Toggle PB5  ***
        }
   }
   return 0;
}

Changed lines indicated by ***
Note that you should not have enabled _BV(TOIE0) because you have no interrupt handler for Timer 0 overflow. Without an interrupt handler the compiler probably generated code to jump to the reset vector.
The interrupt occurs when the timer matches the Compare A amount (not Compare B) so you need an interrupt on the A side.

29824: <p>I know this is a problem that has come up many times but I can't seem to get this code fragment to update the count variable on an ATMEGA328P. I am using an Arduino Uno as a development board, with the LED on pin 13 set to flash for debugging. I have confirmed the timer and LED part work by toggling port B pin 5 in the ISR routine.</p>

<pre><code>#include &lt;avr/io.h&gt;
#include &lt;avr/interrupt.h&gt;

volatile uint8_t count;

void init_100us_tick(void) {
    TCCR0A = _BV(WGM01) | _BV(WGM00);       // WGM mode 7 with OCRA as top
    TCCR0B = _BV(WGM02) | _BV(CS01);        // CLK / 8 prescaler
    TIMSK0 = _BV(OCIE0B) | _BV(TOIE0);      // Interrupt enabled on OCR0A
    OCR0A = 200;                            // 16 MHz / 8 / 200 = 100 us
    sei();                                  // Enable interrupts
}

ISR(TIMER0_COMPB_vect) {
    count++;
}

int main(void) {
    DDRB |= _BV(DDB5);                      // PB5 output
    init_100us_tick();                      // Initialise 100 us tick
    count = 0;                              // In case of micro reset

    for (;;) {
        if (count &gt;= 100) {                 // Every 10 ms
            count = 0;
            PORTB ^= _BV(DDB5);             // Toggle PB5
        }
   }
   return 0;
}
</code></pre>

<p>This is being compiled and burned to an Arduino Uno with the following:</p>

<pre><code>avr-gcc -Os -DF_CPU=16000000UL -mmcu=atmega328p -c -o test.o test.c
avr-gcc -mmcu=atmega328p test.o -o test
avr-objcopy -O ihex -R .eeprom test test.hex
avrdude -F -V -c arduino -p ATMEGA328P -P /dev/ttyUSB0 -b 115200 -U flash:w:test.hex
</code></pre>

<p>I have tried disabling the optimisation with no effect. AVR-GCC is version 4.9.2</p>
 10794: <p>You want CTC mode for that to work. As in:</p>

<pre><code>#include &lt;avr/io.h&gt;
#include &lt;avr/interrupt.h&gt;

volatile uint8_t count;

void init_100us_tick(void) {
    TCCR0A = _BV(WGM01);       // CTC mode 2 with OCRA as top
    TCCR0B = _BV(CS01);        // CLK / 8 prescaler
    TIMSK0 = _BV(OCIE0B) | _BV(TOIE0);      // Interrupt enabled on OCR0B
    OCR0A = 200;                            // 16 MHz / 8 / 200 = 100 us
    sei();                                  // Enable interrupts
}

ISR(TIMER0_COMPB_vect) {
    count++;
}

int main(void) {
    DDRB |= _BV(DDB5);                      // PB5 output
    init_100us_tick();                      // Initialise 100 us tick
    count = 0;                              // In case of micro reset

    for (;;) {
        if (count &gt;= 100) {                 // Every 10 ms
            count = 0;
            PORTB ^= _BV(PORTB5);             // Toggle PB5
        }
   }
   return 0;
}
</code></pre>

<p>That toggles every 10 ms.</p>

<hr>

<p><strong>(Edited to add)</strong></p>

<p>The PWM mode you chose will work providing you enable the correct interrupt. This also outputs 10 ms pulses:</p>

<pre><code>#include &lt;avr/io.h&gt;
#include &lt;avr/interrupt.h&gt;

volatile uint8_t count;

void init_100us_tick(void) {
    TCCR0A = _BV(WGM01) | _BV(WGM00);       // Fast PWM mode 7 with OCRA as top
    TCCR0B = _BV(WGM02) | _BV(CS01);        // CLK / 8 prescaler
    TIMSK0 = _BV(OCIE0A);                   // Interrupt enabled on OCR0A  ***
    OCR0A = 200;                            // 16 MHz / 8 / 200 = 100 us
    sei();                                  // Enable interrupts
}

ISR(TIMER0_COMPA_vect) {                    // Compare A vector ***
    count++;
}

int main(void) {
    DDRB |= _BV(DDB5);                      // PB5 output
    init_100us_tick();                      // Initialise 100 us tick
    count = 0;                              // In case of micro reset

    for (;;) {
        if (count &gt;= 100) {                 // Every 10 ms
            count = 0;
            PORTB ^= _BV(PORTB5);           // Toggle PB5  ***
        }
   }
   return 0;
}
</code></pre>

<p>Changed lines indicated by <code>***</code></p>

<p>Note that you should <strong>not</strong> have enabled <code>_BV(TOIE0)</code> because you have no interrupt handler for Timer 0 overflow. Without an interrupt handler the compiler probably generated code to jump to the reset vector.</p>

<p>The interrupt occurs when the timer matches the <strong>Compare A</strong> amount (not Compare B) so you need an interrupt on the A side.</p>
