select f.name_file 
from files f,
(
select file_id
from downloads
group by file_id
having max(date) < (now() - interval 3 months))
) d
where f.id = d.file_id

mysql> create table uploads(id int, name_file text, date_upload date);
Query OK, 0 rows affected (0.03 sec)

mysql> create table downloads(id int, file_id int, date_download date);
Query OK, 0 rows affected (0.02 sec)

mysql>
mysql> insert into uploads (id, name_file, date_upload) values
    ->   (1,'file 1','2013-01-01')   -- скачивался в посл. 3 мес., не удалять
    -> , (2,'file 2','2013-01-02')   -- не скачивался в посл. 3 мес., удалять
    -> , (3,'file 3','2013-01-03')   -- не скачивался вообще, удалять
    -> , (11,'file 11','2013-09-11') -- скачивался, не удалять
    -> , (12,'file 12','2013-09-12');-- не скачивался, не удалять
Query OK, 5 rows affected (0.00 sec)
Records: 5  Duplicates: 0  Warnings: 0

mysql>
mysql> insert into downloads(id, file_id, date_download) values
    ->   (1,1,'2013-01-01')
    -> , (2,1,'2013-09-09')
    -> , (3,2,'2013-01-01')
    -> , (4,2,'2013-02-02')
    -> , (5,11,'2013-09-12');
Query OK, 5 rows affected (0.00 sec)
Records: 5  Duplicates: 0  Warnings: 0

mysql>
mysql> select id, name_file, date_upload from uploads;
+------+-----------+-------------+
| id   | name_file | date_upload |
+------+-----------+-------------+
|    1 | file 1    | 2013-01-01  |
|    2 | file 2    | 2013-01-02  |
|    3 | file 3    | 2013-01-03  |
|   11 | file 11   | 2013-09-11  |
|   12 | file 12   | 2013-09-12  |
+------+-----------+-------------+
5 rows in set (0.00 sec)

mysql> select id, file_id, date_download from downloads;
+------+---------+---------------+
| id   | file_id | date_download |
+------+---------+---------------+
|    1 |       1 | 2013-01-01    |
|    2 |       1 | 2013-09-09    |
|    3 |       2 | 2013-01-01    |
|    4 |       2 | 2013-02-02    |
|    5 |      11 | 2013-09-12    |
+------+---------+---------------+
5 rows in set (0.00 sec)

mysql>
mysql> select q.id
    -> from
    -> (
    -> select id, date_upload d from uploads
    -> union
    -> select file_id, date_download from downloads
    -> ) q
    -> group by q.id
    -> having max(d) < (now() - interval 3 month);
+------+
| id   |
+------+
|    2 |
|    3 |
+------+
2 rows in set (0.00 sec)