We should consider changing the server configuration on drawable.gnome.org so that tables default to InnoDB. InnoDB is really just a better backend than MyISAM in almost every way - the obvious way being that it supports transactions. And it's pretty clearly the future direction for storage engines for MySQL.

The only real downside I know is that we have to dump InnoDB tables for backup rather than using mysqlhotcopy, but our DB backup scripts already handle this, and dump backups actually tend to perform pretty well compared to  mysqlhotcopy (much smaller data size for a gzip'ed dump in most cases.)

Application affects:

 - It won't affect existing applications tables
 - Applications that really care (bugzilla wants some giant non-transactional tables to be MyISAM) will take care of themselves
 - Applications that don't care get a better database