How to distinguish between custom modules and contrib modules?
If you want know which module has been upgraded or not and what things upgrade in module then you can use hacked module of drupal. 

Go to hacked module configuration and click on "list project" Let it do the work.It will process the modules and will check for the changes.

Once it completes the process you will get a list of module along with the number of changes done in the modules.

Now open the directory sites/all/modules/ and check the modules which are displayed in the list you got after hacked process.The listed modules in the result are the contrib modules and rest of the modules should be custom.