I would not assume the disks need to be defragged without other evidence. There are many components that can affect the performance of SAN storage. PCI-e is a faster bus architecture. However, it is unlikely that would increase your performance unless you are running dual-port 4Gb/s host bus adapters (HBA's). What type of storage array is it? What is the speed of your SAN switches, or are you using direct connect? What is the speed of the storage array's fiber channel ports? How many fiber connections does each server have, and how many connections does the array have? If your servers have multiple connections are you using some type of load balancing? If you have SAN switches have you looked at the per port performance to ensure you are not hitting any bottlenecks on the switch? In general SAN boot adds complexity and can make the servers more difficult to manage. I typically only use SAN boot if the server is not capable of housing internal disks, or it is needed for a disaster recovery scenario to replicate the boot drives to another site. Another issue that can degrade performance is swap. If you have no internal drives, and your servers have insufficient memory they could be swapping out to the storage array which can degrade performance. If you are running Windows 2003 you should look into the StorPort drivers as that can increase performance, and if the servers have more than one connection you should look into Multi-Path I/O (MPIO) unless the array offers a proprietary multi-pathing software.