Command insertion and reordering at the same storage controller

The invention relates to a method and apparatus for reordering, at a disk drive controller, a received sequence of read and write commands. The reordering can be system driven so that the system, when a command stalls, examines the command queue for another command to execute. Alternatively, the command queue itself can be reordered depending upon the expected time it takes for various commands to execute. Reordered commands can be flagged so that they cannot be reordered again. The resulting increase in throughput and efficiency occurs without reference to the particular disk drive or disk drive array configuration to which the controller is connected.