Question

SELECT * FROM `groupon-spain-6sep-2011`, `Hoja1`,`GroupaliaJuly2011` 
WHERE `groupon-spain-6sep-2011`.`code`= 5654 
    OR  `Hoja1`.`code` = "5654 
    OR `GroupaliaJuly2011`.`code` = 5654

Answer 1

You are missing any join condition relating the tables to each other so are doing a cartesian join of 3 tables.

I recommend always using explicit join syntax

SELECT *
FROM   `groupon-spain-6sep-2011`
       JOIN `hoja1` ON `groupon-spain-6sep-2011`.foo=`hoja1`.foo
       JOIN `groupaliajuly2011` ON `groupaliajuly2011`.`foo` = `hoja1`.foo
WHERE  `groupon-spain-6sep-2011`.`code` = 5654
        OR `hoja1`.`code` = 5654
        OR `groupaliajuly2011`.`code` = 5654  

Although it is possible that you might be wanting a Union here I think anyway?