you can delete the WAP service books.
this will remove all folders but "Links" (RIM's conrtibution) and "Blackberry Bookmarks", plus those you added yourself. the t-zones and "Carrier Bookmarks" (4.5) will return periodically as the Service Books are pushed back to your handset. just delete them again.
there was a thread way back that specifically listed the Service Books to delete, but i've never been able to locate it again whenever this question arises. a title search for "bookmarks" resulted in this thread
and this thread
(and many many more, though not the one i wanted!