Neil has it right. "Shadow systems" are a nightmare for IT, not only because it creates havoc among the team to allocate resources to processes never documented, but also because IT gets left with a bad reputation if they are perceived to be obstructive to adoption.
What's an enterprise technology group to do? The best approach would first involve understanding the organization's technology portfolio from top to bottom. Once IT has a good grip of the capability of the tools it has on its official bench, then it should see what shadow systems and "mickey mouse" software are out in the field. If such systems are discovered among users, a collaborative dialogue should occur where IT and the usergroup can compare capabilities and deliverables of the enterprise version (if it exists) and the self-built solution.
Many times, the frustration lies in usability problems or inflexibility of the enterprise application. Sometimes no such application exists to assist the user. In these cases, most users understand that tailoring some enterprise software to the groups' needs is a time-consuming and expensive project. Shadow systems then appear because (1) they're easily built, (2) they're faster to deploy, and (3) easy to customize.
Most agile IT groups are able to identify the sophisticated users of the bunch and work closely with them to synergize their workflow ideas with existing enterprise software or create connectors between the shadow system and the enterprise application (hopefully well-documented APIs exist). Creative and resources CIOs and their teams should also be able to spot best-of-breed off-the-shelf/SaaS systems similar to the users' solutions and use those instead —those tend to have flexible UIs and a wealth of enterprise APIs.
if If there is no resolution, the group's issues may need to be taken to a higher level as these may be symptoms of a bigger workflow problem that is hindering productivity.