Percona Server for MySQL is a distribution of MySQL with some proprietary tweaks designed for high performance and availability. I use the Percona Server distribution when possible, along with Percona tools such as backup and recovery and monitoring tools.
Percona Server is fully compatible with the base MySQL distribution and has a consistent version numbering scheme. The primary difference between base MySQL and the Percona distribution is that you have clearly-defined options for commercial support and advanced tools with Percona that you don't have with MySQL.