With internal applications you likely won't have concerns about domain name availability, trademarks, etc., so how about a simple, plain English naming scheme, e.g., "Timesheet," "Expenses," "Inventory"?
There are often several systems being used concurrently that do the same thing: either due to different departments reinventing the wheel, or by somebody rewriting an application without retiring the previous one.
True, but that sounds like "security through obscurity" with regard to naming conflicts--two departments could both invent the same acronym as easily as a plain English equivalent (there must be a ton of "CMS" systems out there, considering "case" and "content" management).
As always it's a people problem that requires communication and coordination (and until that happens we're stuck with CLOTS, BUGR, and NIPL).