Why does a SATA hard drive have jumpers?

Some SATA drivers have jumpers for extra features, or for troubleshooting.

Example from the manual of a Western Digital SATA disk:

Set the Jumpers

The default setting for WD SATA hard drives varies depending on the model. To determine the default setting for your drive, look at the drive label on the top of the drive.

DO NOT change the default setting if you intend to use the drive in a desktop computer.

Change the jumper settings ONLY if you intend to use the drive in an enterprise storage environment. For more information on these advanced settings, obtain the full version WD SATA Installation Guide at support.wdc.com.

SSC_DIS Mode (Default) — Enable or disable the spread spectrum clocking feature. Default setting is disabled.

OPT1 — Only for factory use.

OPT2 — Only for factory use.

On SATA-II drives, a jumper is sometimes used to set the drive into SATA-I mode for compatibility with older controllers.

Some SATA drives have jumpers to enable/disable 3Gb/s functionality or other backwards compatibility items.

See for example this.

On a Seagate ST3500320AS, there are four pins in the jumper block. You put a jumper between two of them to limit the drive to 1.5Gb/s instead of 3Gb/s, as explained in the manual. But what are the other two?

As shown on this page, the other two pins (plus the nearest of the pair of pins used to limit the drive speed, which is a ground) make a serial port, which talks directly to the drive firmware!