To get a list of apps that are not in a Registered Repository or PPA do this:
sudo apt-get install apt-show-versions
apt-show-versions | grep 'No available version'
That should output text like this:
app1 126.96.36.199 installed: No available version in archive
app23 0.3.6 installed: No available version in archive
app332 7.0.9377 installed: No available version in archive
For me this worked and showed three apps I installed using DEB packages and weren't available in a Repo or PPA.
Do remember though that it's impossible to check for all programs, only the ones that went through
dpkg. For instance, some apps are installed by simply extracting them into the correct folders, or others use a standalone installer bin or script. So the best way is for you yourself to keep a list of apps you installed via any method other than APT.