Among the thousands of Linux/m68k installations, there are several organizations who use Linux/m68k in their commercial or research endeavors:
The European Synchrotron Research Facility in Grenoble, France, is using Linux/m68k on several Motorola VME single-board computers with the hope of getting more out of their existing VME installation. You can read more about their projects at their Linux on VME page. (A synchrotron is a type of particle accelerator.)
BVM Ltd. is offering Linux/m68k as an alternative operating system to OS/9 on their VME single-board computers.
Several public web servers are running on Linux/m68k boxes, including http://amiga.nvg.org/ and http://www.uk.linux.org/.