MySQL: How to find MySQL 5.1 (with built-in InnoDB) or MySQL 5.1 (with InnoDB-plugin)?
If it's a plugin then you'll see variable innodb_version:

mysql&gt; show variables like 'innodb_version';
+----------------+----------------+
| Variable_name  | Value          |
+----------------+----------------+
| innodb_version | 5.5.35-rel33.0 |
+----------------+----------------+


InnoDB as a plugin had more features and was more actively developed. That happened due to historical reasons (at that time MySQL was owned by Sun and InnoDB was owned by Oracle). 

I wouldn't recommend using 5.1 as it's EOL. 5.1 isn't any faster than 5.5 or 5.6. Why would it be if the huge team in Oracle works on InnoDB  and 5.5 and 5.6 are great releases. It reminds me common myth "MyISAM is faster than InnoDB".