And given that of all the storage engines supported by MySQL, INNODB is the only one that has both power *and* enforces referential integrity, I would definitely go with it. After all, any other major DB is going to do all that. MyISAM is really best reserved for what I would call "real time" work. Where you need to squeeze out ever last drop of performance.
An optimist sees the glass as half full.
A pessimist sees the glass as half empty.
A realist drinks it no matter how much there is.