Workbench -> Preferences is better then Window ->
Preferences, but I think that a top level menu dedicated explicitly to
customization would very convenient.
My choice is
extendable Configure menu where Preferences would land and
no Window menu.
I would also
add the ability to start Preferences dialog with favorite topic Preferences page
selected on the tree.
This way a
perspective will be able to give user shortcuts to the most important
settings from this perspective point of