Mostrar tablas por motor en MySQL

Si desea los resultados de una sola base de datos

SELECT TABLE_NAME FROM information_schema.TABLES
    WHERE TABLE_SCHEMA = 'dbname' AND engine = 'InnoDB';

Otros ejemplos aquí.

Todas las tablas por motor (excepto las tablas del sistema):

SELECT TABLE_SCHEMA as DbName ,TABLE_NAME as TableName ,ENGINE as Engine 
FROM information_schema.TABLES 
WHERE ENGINE = 'MyISAM' -- or InnoDB or whatever
AND TABLE_SCHEMA NOT IN('mysql','information_schema','performance_schema');

Todas las tablas excepto el motor (excepto las tablas del sistema):

SELECT TABLE_SCHEMA as DbName ,TABLE_NAME as TableName ,ENGINE as Engine 
FROM information_schema.TABLES 
WHERE ENGINE != 'MyISAM' -- or InnoDB or whatever
AND TABLE_SCHEMA NOT IN('mysql','information_schema','performance_schema');

Si algunos tienen problema y quieren ver en qué DB se encuentran las tablas con motor específico

SELECT 
        (SELECT group_concat(TABLE_NAME) 
            FROM information_schema.TABLES
            WHERE TABLE_SCHEMA = 'database1' 
            AND engine = 'MyIsam'
        ) as database1, 
        (SELECT group_concat(TABLE_NAME) 
            FROM information_schema.TABLES
            WHERE TABLE_SCHEMA = 'database2' 
            AND engine = 'MyIsam'
        ) as database2,
        (SELECT group_concat(TABLE_NAME) 
            FROM information_schema.TABLES
            WHERE TABLE_SCHEMA = 'database3' 
            AND engine = 'MyIsam'
         ) as database3;

Saludos.