The difference is, when using MyISAM, you need to write your connstraint logic yourself, which has several drawbacks (you're likely to introduce bugs, it will be separated from database, etc..). With InnoDB, you're using well known and tested code (made in Oracle BTW

) to do same thing.
FK Constraints is not the most important difference between MyISAM and InnoDB. InnoDB is fully ACID compliant, which has several benefits: you can use transactions to avoid race conditions, InnoDB tables are crash safe (no more REPAIR TABLE).
InnoDB also seems to be getting more and more efficient with each new version, although the results will vary greatly depending on usage (mostly on writes/reads ratio for a table).