I realize this is pointing more to a hardware problem but since it happens with ANY drive, ANY controller card, ANY cable, and even USB CD drives, I'm holding out hope isn't not my motherboard.

The problems vary, my current active problem:

[mcarter@whitestar ~]$ eject /dev/sr1
eject: unable to eject

To resolve I'll need to completely POWER OFF the computer. (a reboot won't always work)

Other problems the drive will eject but won't detect the CD/DVD/Blu-Ray. Switching the same media to another drive it will work. Again a full POWER OFF and it starts working again.

Other times I get read errors all over the place... and again a full POWER OFF and it's working again.

Only constent is time. If I watch several DVD's before a reboot... the problem start happening.

Anyone have any ideas where to look? Is there a way of rebooting the drive (asside from unplugging it, which works well for USB drives)

Chances are there is a process holding a file open on the drive. As long as something is accessing the drive, it won't eject.

Check out the lsof command..some examples here:
http://www.thegeekstuff.com/2012/08/...mand-examples/