Hopefully by now you've realized that in order to manage your software (or other IT assets) you need to have an inventory tool. As you will know from my other posts, you can't stop there...but it is a good place to start.
However; you need to understand your tool and how it reports data to you. Otherwise you might get an ugly surprise later on down the road when you find software installed on your systems that wasn't showing on your reports!
Inventory tools have a database of software titles associated with publisher and typically associated with a flag to indicate if it is licensable software (versus freeware, etc). The completeness of this database is the biggest value to you of the tool. With most tools if an executable is not in this database than it gets grouped into a "Misc" category and will fall into an exception report, a "catch all" report or might not be reported at all.
This could include new releases from publishers or simply publishers that your tool publisher doesn't categorize. These "unidentified" programs can cause you a lot of headaches - from a security, licensing and support angle.
Most inventory tools are updated on an ongoing basis as the publisher becomes aware of new software, but if you're not keeping current on your maintenance with that software you might not be getting this updated information.
Protect yourself - keep your maintenance current on any inventory tools you use, check the frequency of the tool publishers updates and include a check of "Misc" or "Catch All" software reports in your Software Asset Management process.
Additionally, if you are concerned about potential risk in this area you might want to consider having all of your software identified. Software ID Technologies has services that will identify all software in your environment. We've teamed with them on a number of engagements and they do a good job of taking the mystery out of those "unidentified" applications.