Percona has recently released some of their performance patches for Mysql 5.1. Previous to these patches were only available for the 5.0.x codebase.
You can read more about it here. The link also provides from interesting benchmarks as well, pitting these patches vs the standard storage engine setup.
To be clear, these patches work against the built in version of Innodb with comes standard with the Mysql server.
You can xtradb if you wish to use some of the Percona patches that pertain to the Innodb plugin that is offered by Innobase