Not all the tables in Magento database uses INNODB engine.
Here are the tables, which use MYISAM engine,
catalogsearch_fulltext
log_customer
log_quote
log_summary
log_summary_type
log_url
log_url_info
log_visitor
log_visitor_info
oscommerce_orders
oscommerce_orders_products
oscommerce_orders_status_history
oscommerce_orders_total
paygate_authorizenet_debug
paypal_api_debug
product_alert_stock
sendfriend_log
Article source: http://www.learnmagento.org/magento-tutorials/tables-using-myisam-engine-on-magento-database/