You are missing a setting in your mysql configuration. Since you have compiled in support for InnoDB, you must either completely configure it, or turn it off. If you do not wish/need to use it, then skip-innodb is the correct choice.
If you wish to use InnoDB, you must set a default path for it (even when specifying file per table, which you aren't). The default path is set via the innodb_data_file_path variable, something similar to the following would suffice:
innodb_data_file_path = ibdata1:10M:autoextend:max:128M
For more information on InnoDB, please see the MySQL manual:
http://dev.mysql.com/doc/refman/5.0/en/innodb-configuration.html
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