Ricky,
In my experience and how I understand it:
MyISAM - you use it when most of your applications
or datas use in this table are text or VACHAR data types.
One advantage is it is fast speed in text searches.
InnoDB - you use this Engine table types when
your datas or when you derive datas to this table
is calculated. Use this when your calculation to store
the result to these datas uses memory. Like a memory function
in a calculator.
Also, the new features of the current version of MySQL currently 5.0 will only apply to InnoDB table engine. This includes Store Procedures, Triggers, Sub-Queries, Temporary Tables and more.
i hope this helps,
John
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