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?

As of the date last updated (see top), 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" and "Mid-2010" Mac Pro models can "unofficially" support a fifth hard drive in the second 5.25" optical drive bay as well. With the OWC Multi-Mount line, in fact, there are a variety of options for SSDs and different sized drives in the 5.25" optical bay or bays.

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" line and pages 68-73 for the "Mid-2010").

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" and "Mid-2010" 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?