Of course you should not be deploying applications, but rather packages in your ConfigMgr 2012 (SCCM) task sequences. But if you do, you can use this little PowerShell script to list applications that have the AutoInstall property set to True, meaning being configured for task sequence deployment.
The Script
$AppList = Get-CMApplication
foreach ($App in $AppList)
{
if ($App.SDMPackageXML -like '*<AutoInstall>true</AutoInstall>*')
{
Write-Output $App.LocalizedDisplayName
}
}
Note #1: If you want to list applications not configured for AutoInstall, just change the operator to -notlike.
Note #2: If you have many applications (like hundreds), the Get-CMApplication cmdlet is quite slow. To get some speedy result, you can also query the fn_ListLatestApplicationCIs(1033) SQL function directly in the ConfigMgr database. Fellow MVP Torsten Meringer have a nice post (in German) here: http://www.mssccmfaq.de/2013/08/28/applications-die-in-einer-task-sequenz-installiert-werden-duerfen/

Running the script.
The above script enumerates all applications that have the below setting (Allow this application to be installed from the Install Application task sequence without being deployed).

An application configured for task sequence deployment.
/ Johan
Of course, in Contoso-land everything works, it's in the real world you run into issues.
Most issues are fixed in ConfigMgr 2012 R2 CU2, but there have been plenty of fixes for this since release of ConfigMgr 2012 to address issues with apps in a task sequence…
Anyway, here is a good read: http://www.david-obrien.net/2014/04/05/applications-vs-packages-configmgr-package-model-wont-go-anywhere/
/ Johan
"Of course you should not be deploying applications, but rather packages in your ConfigMgr 2012 (SCCM) task sequences."
I've heard a dozen non-Microsoft people say that. I've asked two separate MS consultants here helping us set up a 2012 R2 environment, and they both insist there is no issue. Since I haven't started OSD yet, I have no first hand experience and honestly, probably no choice in the matter. What is the reasoning behind this?