Not sure about 'best', but the way I go about it is to measure the total time required for an application to complete a task, then attempt to measure the indivi

Not sure about 'best', but the way I go about it is to measure the total time required for an application to complete a task, then attempt to measure the individual components (time spent in PHP, data transfer, rending on client side etc.) and keep narrowing it down until you find the exact cause, such as a database query which requires optimisation.