The database format InnoDB is becoming more mature since Mysql 4.1.
However the MyISAM is faster for most applications. The main
advantage of InnoDB is that it enable row locking versus table locking for
MyISAM write.
If you applications performs many simultaneous writes to the same table InnoDB,
it might be a better choice for that particular table. However most web site do
not have this issue. Even on a busy forum site (for example: a vbulletin site)
concurrent writes are pretty rare. If you start getting constant database errors
when reading/wrinting to large table tables it might be time to upgrade that
table to InnoDB.