which mysql version to use - 5.1 or 5.5?
There is no substitute of tuning MySQL. Left unconfigured, there are cases when even MySQL 4.1 outperforms MySQL 5.x on the same level playing field.

Here are my past posts on the subject


Oct 05, 2011 : Query runs a long time in some newer MySQL versions
Nov 24, 2011 : Why mysql 5.5 slower than 5.1 (linux,using mysqlslap)
Feb 08, 2012 : MySQL 5.5 perfomance (StackOverflow)
Feb 22, 2012 : MySQL 5.1 vs MySQL 5.5 (5.1 twice as fast) (ServerFault)
Jul 16, 2012 : decreased performance of stored procedure when migrated from mysql server 5.0 to 5.5


Bottom Line

You should always use the most stable release of MySQL because there are just certain bug and features that are fixed that do not carry over to the next major release.

Note that


MySQL 5.0 is up to 5.0.96, but the bugs that MySQL 5.5 Addressed still reside in 5.0.96
MySQL 5.1 is up to 5.1.67, but the bugs that MySQL 5.5 Addressed still reside in 5.1.67


There are many exciting things that MySQL 5.5 features tuning for the following:


Multicore Processing


May 26, 2011 : About single threaded versus multithreaded databases performance
Sep 12, 2011 : Possible to make MySQL use more than one core?
Sep 20, 2011 : Multi cores and MySQL Performance

Semisynchronous Replication


Aug 05, 2011 : Is MySQL Replication Affected by a High-Latency Interconnect?
Oct 29, 2012 : Installing and enabling both master and slave semisynchronous plugins on same server

Buffer Pool Instances : Feb 12, 2011 : How do you tune MySQL for a heavy InnoDB workload?