Which part of of a hard drive has the highest throughput, beginning or end of drive?

Most commonly a partition at the "end" of the disk is on the inner-most part of the platter, and will have the slowest transfer speed. Not all drives are guaranteed to work this way however.

The farther away from the inside of the disk platters you go, the higher the velocity of the head relative to the platter is. Therefore you can see peak sequential transfer speeds of up to 2X when comparing the outermost area of a hard drive platter to the innermost. This can be verified with a utility such as HDTune.

To take advantage of this, those seeking the highest performance from platter drives will often partition only the start of the drive, therefore formatting the drive to a lower capacity, utilizing the faster part of the hard drive. This process is called 'short-stroking'.