Yes. You just need to make sure that the JAR with custom L&F classes is in the classpath and specify the --laf <class> option when starting NB.
To add the JAR with L&F classes to the classpath, use the --cp:p <jar-file> option.
Alternatively, to force NB to use the Java cross-platform L&F (Metal/Ocean), specify javax.swing.plaf.metal.MetalLookAndFeel as the L&F class.
Note: NetBeans is not being regularly tested with alternate look and feel implementations. Various implementations may or may not work well.
netbeans --cp:p C:\looks-1.2.2.jar --laf com.jgoodies.plaf.plastic.PlasticXPLookAndFeel
netbeans --cp:p C:\winlaf-0.5.1.jar --laf net.java.plaf.windows.WindowsLookAndFeel
Edit:
/Applications/NetBeansIDE5.0Beta.app/Contents/Resources/NetBeans/etc/netbeans.conf
so that the line beginning netbeans_default_options includes the option:
--laf javax.swing.plaf.metal.MetalLookAndFeel
Edit from your NB installation directory:
etc/netbeans.conf
so that the line beginning netbeans_default_options includes the option:
--laf com.sun.java.swing.plaf.gtk.GTKLookAndFeel
See also: NetBeans 6.0 supports the Substance Look and Feel
Applies to: NetBeans 4.0, 4.1, 5.0, 5.5, 6.0
Platforms: All (specific L&F implementations may work on specific platforms only).