hmmm ...as AdobeShinobi pointed, magento seems to be using a lot of Foreign Key references and MYSQL as of now does not seem to be supporting Foreign key references yet (refer
But I do believe that MYISAM would be more approriate for an ecommerce system where the search functionality is more important and performance has top priority. Well atleast for the search related tables and on Attribute tables where MYISAM offers a significant performance boost through its index caching. A programmatic check in code may be more optimized by than enforcing referential integrity through foreign keys for the following tables atleast -
All catalog tables like catalog_product_entity, catalog_product_entity_varchar, catalog_product_entity_text, etc
All EAV attribute tables
In retrospect, I wonder why the INNODB implementation was preferred for these tables.