select
TABLES.TABLE_SCHEMA as `Database`,
TABLES.table_name as `Table`,
columns.column_name as `Primary Key`,
CONCAT('ALTER TABLE `',TABLES.TABLE_SCHEMA,'`.`',TABLES.table_name,'` ORDER BY `',columns.column_name,'`; ALTER TABLE `',TABLES.TABLE_SCHEMA,'`.`',TABLES.table_name,'` engine=InnoDB;') as `Command`
from
information_schema.TABLES
left join information_schema.columns
on columns.table_name = TABLES.table_name
where
TABLES.ENGINE = "MyISAM"
and TABLES.TABLE_SCHEMA != "information_schema"
and TABLES.TABLE_SCHEMA != "mysql"
and columns.column_key = "PRI"
and TABLES.table_name = "webdb"
and concat(TABLES.TABLE_SCHEMA,".",TABLES.TABLE_NAME) not in
(
SELECT
concat(STATISTICS.TABLE_SCHEMA,".",STATISTICS.TABLE_NAME) as `Fulltable Name`
FROM
information_schema.STATISTICS
WHERE
STATISTICS.index_type = "FULLTEXT"
ORDER BY
1
)
order by
TABLES.TABLE_SCHEMA,
TABLES.table_name;


SELECT CONCAT('ALTER TABLE `',table_schema,'`.`',table_name,'` ORDER BY primary_key_column; ALTER TABLE `',table_schema,'`.`',table_name,'` engine=InnoDB;') FROM information_schema.tables WHERE TABLE_SCHEMA='xbmc-tv' AND ENGINE = 'MyISAM';


SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ORDER BY primary_key_column; ALTER TABLE ',table_schema,'.',table_name,' engine=InnoDB;') FROM information_schema.tables WHERE TABLE_SCHEMA='my_database' AND ENGINE = 'MyISAM';

Replace 'my_database' with your DB name.

Originated from:
http://codesnippets.joyent.com/posts/show/1451

Somehow, I have some of the tables with Engine Type INNODB, and other MyISAM. : (

When I try to manually change one of them, I get Error (121) with some text prior to it.

Thanks for the assist

ALTER TABLE tablename ORDER BY 'primary_key_column';

Instead, use:

ALTER TABLE tablename ORDER BY primary_key_column;

(Note the removal of the single quotes)