Why you would use MyISAM:
– If you need to make use of “full text search”, although no prebuilt application will use FTS as MyISAM is the only engine to support it.
– The application is mostly for reporting purposes, data is loaded at off hour times in batch mode, as opposed to users coming in and updating frequently.
– SEcurity is not an issue. MyISAM stores all data in flat files that are easily read.
– Native hot backup and check utilities work for this engine since it is MySQL’s proprietery engine.
Why you would use InnoDB:
– Row level locking allows for multiple rows/data sets to be updated at a time without causing problems with the system.
– Enforcement of foreign keys, the only engine that works with MySQL that enforces them.
– uses “data files” similar to the larger DB’s such as SQL Server and Oracle, these are encrypted and therefore more secure.
– purchasing hot backup utility provides a license to use it – your company is theoretically covered if something bad happens.