The two main database types to select from for MySQL are MyISAM or INNO DB.
The main differences are MyISAM allows for MySQL specific features like FULLTEXT searching which some people find very useful. You can also easily back up and other things with MyISAM.
INNO DB on the other hand does row level locking instead of table level locking like MyISAM tables do. So if you have a site that does a lot of locking and gets a lot of traffic INNO DB is probably the way to go (Think of applications like phpAdsNew). You lose MySQL specific features though like FULLTEXT searching.
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