With Oracle SQL Developer 3.2.20.09, i managed to set the custom format for the type DATE this way :
In : Tools > Preferences > Database > NLS
Or : Outils > Préférences > Base de donées > NLS
YYYY-MM-DD HH24:MI:SS
Note that the following format does not worked for me :
DD-MON-RR HH24:MI:SS
As a result, it keeps the default format, without any error.