You can have either a dynamic or a static nodegroup within the NODEGROUP configuration. A static nodegroup contains nodes that have been added manually and you can simply edit the configuration properties to manually remove these. If the nodegroup is dynamic, it assesses a Prognosis record which can use a where clause to determine whether or not it meets specific criteria before it will be added to that nodegroup. For these types of nodegroups, you would need to modify the where clause or possibly make changes to the host system so that is no longer included in that group. For example, if you look at the properties of the 'Windows Systems\Applications\IIS' nodegroup, it's looking for the W3SVC service name in the NTSERVICE record. If you had a node in that group that you did not want to be included, one solution may be to stop the W3SVC from running on that node.
Hope this helps. If you have further questions please let me know!