Anteriormente, eu estava fazendo o seguinte para obter a contagem diária da tabela de relatórios.

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, isso não me dará 0 contagem para datas ausentes.

Então eu finalmente encontrei umsolução ideal para gerar séries de datas entre o período especificado. Mas o próximo desafio que estou enfrentando é associá-lo à minha tabela de relatórios e agrupar a contagem por data.

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 ;

O resultado que estou obtendo é

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
...

Considerando que estou procurando preencher as datas ausentes com 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
...

Outra tentativa que dei foi:

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

Dados mínimos com as consultas acima:http://sqlfiddle.com/#!2/dee3e/6