MyISAM and InnoDB are the most commonly used engines.
MyISAM is slightly faster than InnoDB, and implements the FULLTEXT index which is quite useful for integrating search capabilities.
MyISAM is not transacted and doesn't implement foreign key constraints, which is a major drawback.
But you can use the best of both and create tables with different storage engines. Some software (WordPress, I think) use Inno for most data, like relations between pages, versions etc. Records for the posts contain an ID that links to a record in a separate content table that uses MyISAM. That way, the content is stored in the table that has the best search capabilities, while most other data is stored in tables that enforce data integrity.
If I were you, I'd pick Inno, because it is the most reliable. Only use MyISAM for specific purposes if you need to.
You can configure your database to use InnoDB by default when creating new tables.