For example, you can swap X/O buttons on the PS3 Controller using it as follows:
Use FTP to download /dev_flash2/etc/xRegistry.sys (create a copy just to be safe)
Open with xRegistry.sys Editor
Change the value of setting/system/buttonAssign from 00000000 to 0000001 and click save
Save the file and upload it to /dev_flash2/etc/xRegistry.sys overwriting the existing file
This will permanently change the button layout, no need to go through this process again unless you want to revert back to the original button layout.
Among other things, likely region-free DVD and Blu-ray but time will tell for sure.