What options are available for the second "optical drive bay" on the Mac Pro? How do you install a second optical drive or replace the primary one?

To date (see top of page), the only option Apple offers for the second 5.25" external Mac Pro "optical drive bay" is a second dual-layer SuperDrive.

However, site sponsor Other World Computing sells a variety of optical drives that are compatible with the Mac Pro including internal Blu-ray drives that are capable of both reading and writing Blu-ray media. Unofficially, as OWC also has noted, the "Early 2009" Mac Pro models can "unofficially" support a fifth hard drive in the second 5.25" optical drive bay as well.

Apple provides a PDF with instructions on how to install a second optical drive or replace the primary one in the Mac Pro -- and covers this information in the instruction manuals for each model as well (pages 63-68 for the "Early 2009" model).

The official documentation absolutely should be read before performing an optical drive installation. However, perhaps even better than the official drawings, OWC provides a step-by-step videos of the upgrade process.

This video covers installing an optical drive in the original and "Early 2008" models:

This video covers installing an optical drive in the "Early 2009" Mac Pro models:

Also see: How do you upgrade the hard drives in the Mac Pro models? How many drives of what type are supported?