In System Center 2007 and older deploying software was handled through PACKAGES and as such a category named PACKAGES in SCCM > SOFTWARE LIBRARY > OVERVIEW still exists for backwards compatibility. System Center now uses APPLICATIONS to deploy software and that is what you should move to (or start with, if you are new to SCCM).
The APPLICATIONS logic allows more options, like Supercedence, Requirements and Global Conditions. Contrary to some reports, APPLICATIONS support both .EXE and .MSI sources.
As usual, there is always an exception to the rule, and in this case PACKAGES do have a feature that APPLICATIONS do not, recurrence schedule, which few people will care about.
See our simplified explanation of how to deploy an .MSI via System Center Configuration Manager 2012 R2.
If you want to argue with someone about features, take a look at THIS Microsoft Support thread.