MySQL+Web-App Performance Issues using different servers
The OS even shows that we have an IO WAIT problem.

We think we have found the issue - the LSI MegaRAID SAS 9260-8i (Supermicro 
SMC2108) RAID adapter. Either we have it configured incorrectly or it's just a poor performer.

We stumbled onto this blog:
http://artipc10.vub.ac.be/wordpress/2011/09/12/megacli-useful-commands/

and disabled the Patrol Read function and it increased our TPS by almost 130/second.

Trying to solicit tweaking recommendations here: https://askubuntu.com/questions/304488/tweaking-recommendations-for-smc2108-lsi-megaraid-sas-9260-8i-raid-adapter

This link http://www.randombugs.com/linux/tuning-linux-system-database.html was
very very useful. We implemented these changes which resulted in significant TPS improvements.