SELECT DISTINCT SCHEMA_NAME AS `database`
    FROM information_schema.SCHEMATA
   WHERE  SCHEMA_NAME NOT IN ('information_schema', 'performance_schema', 'mysql')
   ORDER BY SCHEMA_NAME
gets you a list of all the non-MYSQL databases on your system.
  SELECT TABLE_SCHEMA AS `database`,
         TABLE_NAME AS `table`
    FROM information_schema.TABLES
   WHERE TABLE_TYPE = 'BASE TABLE'
   ORDER BY TABLE_SCHEMA, TABLE_NAME
gets you a list of all the actual tables (excluding SYSTEM VIEWs like the TABLES table, and user-defined views) in all the databases.
Then, you should implement logic in your program to ensure that, for each database, it really is a Magento database before you truncate certain tables. Otherwise, you might become a despised person among your co-workers. :-)
Edit
Here's a stored procedure.  
You need to edit it to do exactly what you need it to do; in particular, it counts rows rather than truncating tables, and it doesn't contain the correct list of log tables. (It would be irresponsible for me to publish such a wildly destructive stored procedure; you should edit it yourself to do the destructive part.)
DELIMITER $$
DROP PROCEDURE IF EXISTS `zap_magento_logs`$$
CREATE PROCEDURE `zap_magento_logs`()
BEGIN
    -- declare variables for database and table names
    DECLARE dbname VARCHAR(128) DEFAULT '';
    DECLARE tbname VARCHAR(128) DEFAULT '';
    DECLARE done INTEGER DEFAULT 0;
    -- declare cursor for list of log tables
    DECLARE log_table_list CURSOR FOR 
      SELECT TABLE_SCHEMA AS `database`,
             TABLE_NAME AS `table`
        FROM `information_schema`.TABLES
       WHERE TABLE_TYPE = 'BASE TABLE'
         AND TABLE_NAME IN 
         (
            'log_customer',
        'log_visitor',
        'log_visitor_info',
        'log_url',
        'log_url_info',
        'log_quote'
         )
       ORDER BY TABLE_SCHEMA, TABLE_NAME;
    -- declare NOT FOUND handler
        DECLARE CONTINUE HANDLER 
        FOR NOT FOUND SET done = 1;
    OPEN log_table_list;
    log_table: LOOP
        FETCH log_table_list INTO dbname, tbname;
        IF done = 1 THEN
        LEAVE log_table;
        END IF;
        -- create an appropriate text string for a DDL or other SQL statement
        SET @s = CONCAT('SELECT COUNT(*) AS num FROM  ',dbname,'.',tbname);
        PREPARE stmt FROM @s;
        EXECUTE stmt;
        DEALLOCATE PREPARE stmt; 
    END LOOP    log_table;
    CLOSE log_table_list;
END$$
DELIMITER ;
You run this by issuing the SQL command
  CALL zap_magento_logs();