How to duplicate a folder exactly

Try doing this the straightforward way :

cp -a src target

from man cp

    -a, --archive
           same as -dR --preserve=all

It preserve rights, symlinks...

Here I tried all the code in my Linux. Seems Rsync proposed by @seanmcl as the right one while others failed to keep owners and/or some special files or a denied result. The exact code is:

$ sudo rsync -aczvAXHS --progress /var/www/html /var/www/backup

Just remember to use just the directory name and not put a slash (/) or a wildcard (/*) at the end of source and target name otherwise the hidden files right below the source are not copied.