What is InnoDB and MyISAM in MySQL ?
I wanted to add that having ability to specify a specific storage engine per table is one of the key strengths of MySQL (besides easy of use and good performance with no tweaking). For all operations where transactions are needed, just stick with InnoDB. However, MyISAM can really speed things up when transactions are not needed in certain situations - and requires less disk space and RAM compared to InnoDB.
That said, InnoDB is getting better all the time:
InnoDB 1.1 Performance and Scalability Enhancements