If you do not want the Nintex Workflow site and site collection Features to show in up in the avaliable Feature list, you can hide them by following these steps. Please note though that after an upgrade of Nintex Workflow, you will need to perform these steps again because the upgrade will overwrite your changes.
1) On each front end server, browse to <sharepoint 12 directory>\Template\Features
2) To hide the site collection Feature: open the NintexWorkflow folder. To hide the site level Feature: open the NintexWorkflowWeb folder.
3) Edit the Feature.xml file in notepad
4) In the main Feature element, find the xml attribute called 'Hidden' if it exists and make it Hidden="TRUE". Add it if it does not exist, setting its value to TRUE.
5) Save the file.
6) Reset IIS
The Feature should no longer display in the list.
If you need to activate it somewhere when it is hidden, you will need to use STSADM.exe
For the site collection Feature:
stsadm.exe -o activatesolution -n nintexworkflow -url http://sitecollectionurl
For the site level Feature:
stsadm.exe -o activatesolution -n nintexworkflowweb -url http://teamsiteurl
regards,
James