You can use MySQL to script it and execute it:
This will convert every InnoDB table in database dbname to MyISAM
CONVERT_SCRIPT=Convert_dbname_InnoDB_to_MyISAM.sql
mysql -u... -p... -AN -e"SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=MyISAM;') FROM information_schema.tables WHERE table_schema='dbname' AND engine='InnoDB';" > ${CONVERT_SCRIPT}
mysql -u... -p... -A < ${CONVERT_SCRIPT}
This will convert every InnoDB table to MyISAM
CONVERT_SCRIPT=Convert_InnoDB_to_MyISAM.sql
mysql -u... -p... -AN -e"SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=MyISAM;') FROM information_schema.tables WHERE engine ='InnoDB';" > ${CONVERT_SCRIPT}
mysql -u... -p... -A < ${CONVERT_SCRIPT}
If you do not want the conversion of the tables to be replicated to Slaves, just put SET SQL_LOG_BIN=0; as the first line. That way, you can test the conversion in a Master/Slave setup by converting only the Slave first and then the Master later.
This will convert every InnoDB table in database dbname to MyISAM and not replicate to other servers
CONVERT_SCRIPT=Convert_dbname_InnoDB_to_MyISAM.sql
echo "SET SQL_LOG_BIN=0;" > ${CONVERT_SCRIPT}
mysql -u... -p... -AN -e"SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=MyISAM;') FROM information_schema.tables WHERE table_schema='dbname' AND engine='InnoDB';" >> ${CONVERT_SCRIPT}
mysql -u... -p... -A < ${CONVERT_SCRIPT}
This will convert every InnoDB table to MyISAM and not replicate to other servers
CONVERT_SCRIPT=Convert_InnoDB_to_MyISAM.sql
echo "SET SQL_LOG_BIN=0;" > ${CONVERT_SCRIPT}
mysql -u... -p... -AN -e"SELECT CONCAT('ALTER TABLE ',table_schema,'.',table_name,' ENGINE=MyISAM;') FROM information_schema.tables WHERE engine ='InnoDB';" >> ${CONVERT_SCRIPT}
mysql -u... -p... -A < ${CONVERT_SCRIPT}
Give it a Try !!!