How to distinguish between custom modules and contrib modules? We have taken a project where we have to upgrade a site from d6 to d7.

But their module structure is poor, and does not distinguish between custom and contrib modules. We also want to know what's upgradable, and what isn't?

This would be helpful for sending project estimation.

Is there a way to do this using drush perhaps?
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.