How to get list of module folders which can be deleted safely?
Use this:

drush pmi --fields=type,project,title,status,path --format=table|sort


This gives you a module list with five columns:


First is the type of project: module or theme.
Second one is the module project, for exampe views, logintoboggan, admin_menu, etc.
The third one is the installation status: enabled (in use), disabled (not in use but install info in DB) and not installed (it hasn't been installed yet or it have been already uninstalled).
Fourth column is module name. A module downloaded from drupal.org can have several modules inside (the downloaded module is the project and the inside modules are the real modules).
The fifth column is the path to the module.


With this information you can safely remove every project (second column) that all of its modules are in 'not installed' state. 

For example, see this fragment list:

module  job_scheduler  Job Scheduler                enabled        sites/all/modules/contrib/job_scheduler                                                  
module  job_scheduler  Job Scheduler Trigger        not installed  sites/all/modules/contrib/job_scheduler/modules/job_scheduler_trigger                    
module  jquery_update  jQuery Update                enabled        sites/all/modules/contrib/jquery_update                                                  
module  l10n_client    Localization client          enabled        sites/all/modules/contrib/l10n_client                                                    
module  l10n_update    Localization update          enabled        sites/all/modules/contrib/l10n_update                                                    
module  languageicons  Language Icons               enabled        sites/all/modules/contrib/languageicons                                                  
module  ldap           LDAP Authentication          not installed  sites/all/modules/contrib/ldap/ldap_authentication                                       
module  ldap           LDAP Authorization - Roles   not installed  sites/all/modules/contrib/ldap/ldap_authorization/ldap_authorization_drupal_role         
module  ldap           LDAP Authorization           not installed  sites/all/modules/contrib/ldap/ldap_authorization                                        
module  ldap           LDAP Authorization - OG      not installed  sites/all/modules/contrib/ldap/ldap_authorization/ldap_authorization_og                  
module  ldap           LDAP Feeds                   not installed  sites/all/modules/contrib/ldap/ldap_feeds                                                
module  ldap           LDAP Help                    not installed  sites/all/modules/contrib/ldap/ldap_help                                                 
module  ldap           LDAP Query                   not installed  sites/all/modules/contrib/ldap/ldap_query                                                
module  ldap           LDAP Servers                 not installed  sites/all/modules/contrib/ldap/ldap_servers                                              
module  ldap           LDAP SSO                     not installed  sites/all/modules/contrib/ldap/ldap_sso                                                  
module  ldap           LDAP Test Module             not installed  sites/all/modules/contrib/ldap/ldap_test                                                 
module  ldap           LDAP User Module             not installed  sites/all/modules/contrib/ldap/ldap_user                                                 
module  ldap           LDAP Views                   not installed  sites/all/modules/contrib/ldap/ldap_views                                                
module  libraries      Libraries                    enabled        sites/all/modules/contrib/libraries 


You can safely remove the ldap module because all modules are not installed but not job scheduler because one of its modules is enabled.