If you do not need JavaDoc API documentation for NetBeans sources, make sure to disable -doc USE flag. Building documentation for NetBeans sources can take a lot of time.
Since netbeans-6.9-r3, you can turn on support for keychain by enabling keychain. If you enable this, you will be able to benefit from keychain in NetBeans when connecting to ssh protected remote repositories. When you start NetBeans (from menu, from run window or from terminal, does not really matter), keychain will be run and keys that you can optionally specify will be added to ssh-agent and you will be prompted for key passwords if the keys are not managed yet. This is the first and last time NetBeans will ask you for key passwords. To specify keys that you want to add to ssh-agent on NetBeans startup, create file keychain-keys.txt in your userdir (by default ~/.netbeans/6.9/) and put on each line single key that you want to load.