Anteriormente estaba haciendo lo siguiente para obtener el conteo por día de la tabla de informes.

SELECT COUNT(*) AS count_all, tracked_on
 FROM `reports`
 WHERE (domain_id = 939 AND tracked_on >= '2014-01-01' AND tracked_on <= '2014-12-31')
 GROUP BY tracked_on
 ORDER BY tracked_on ASC;

Obviamente, esto no me dará un recuento de 0 para las fechas que faltan.

Entonces finalmente encontré unsolución óptima para generar series de fechas entre el rango de fechas dado. Pero el próximo desafío al que me enfrento es unirlo a mi tabla de informes y obtener el recuento agrupado por fecha.

select count(*), all_dates.Date as the_date, domain_id
from (
    select curdate() - INTERVAL (a.a + (10 * b.a) + (100 * c.a)) DAY as Date
    from (select 0 as a union all select 1 union all select 2 union all select 3 union all select 4 union all select 5 union all select 6 union all select 7 union all select 8 union all select 9) as a
    cross join (select 0 as a union all select 1 union all select 2 union all select 3 union all select 4 union all select 5 union all select 6 union all select 7 union all select 8 union all select 9) as b
    cross join (select 0 as a union all select 1 union all select 2 union all select 3 union all select 4 union all select 5 union all select 6 union all select 7 union all select 8 union all select 9) as c
) all_dates
inner JOIN reports r
    on all_dates.Date >= '2014-01-01'
  and all_dates.Date <= '2014-12-31'
where all_dates.Date between '2014-01-01' and '2014-12-31' AND domain_id = 939 GROUP BY the_date order by the_date ASC ;

El resultado que obtengo es

count(*)    the_date    domain_id
46  2014-01-01  939
46  2014-01-02  939
46  2014-01-03  939
46  2014-01-04  939
46  2014-01-05  939
46  2014-01-06  939
46  2014-01-07  939
46  2014-01-08  939
46  2014-01-09  939
46  2014-01-10  939
46  2014-01-11  939
46  2014-01-12  939
46  2014-01-13  939
46  2014-01-14  939
...

Mientras que estoy buscando completar las fechas faltantes con 0

algo como

count(*)    the_date    domain_id
12  2014-01-01  939
23  2014-01-02  939
46  2014-01-03  939
0   2014-01-04  939
0   2014-01-05  939
99  2014-01-06  939
1   2014-01-07  939
5   2014-01-08  939
...

Otro intento que hice fue:

select count(*), all_dates.Date as the_date, domain_id
from (
    select curdate() - INTERVAL (a.a + (10 * b.a) + (100 * c.a)) DAY as Date
    from (select 0 as a union all select 1 union all select 2 union all select 3 union all select 4 union all select 5 union all select 6 union all select 7 union all select 8 union all select 9) as a
    cross join (select 0 as a union all select 1 union all select 2 union all select 3 union all select 4 union all select 5 union all select 6 union all select 7 union all select 8 union all select 9) as b
    cross join (select 0 as a union all select 1 union all select 2 union all select 3 union all select 4 union all select 5 union all select 6 union all select 7 union all select 8 union all select 9) as c
) all_dates
inner JOIN reports r
    on all_dates.Date = r.tracked_on
where all_dates.Date between '2014-01-01' and '2014-12-31' AND domain_id = 939 GROUP BY the_date order by the_date ASC ;

Resultados:

count(*)    the_date    domain_id
38        2014-09-03     939
8         2014-09-04     939

Datos mínimos con las consultas anteriores:http://sqlfiddle.com/#!2/dee3e/6