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So I was going to back up my home folder by copying it to an external drive as follows:

sudo cp -r /home/my_home /media/backup/my_home

With the result that all folders on the external drives are now owned by root:root. How can I have cp keep the ownership and permissions from the original?

sudo cp -rp /home/my_home /media/backup/my_home

From cp manpage:

 -p same as --preserve=mode,ownership,timestamps

 --preserve[=ATTR_LIST]
 preserve the specified attributes (default: mode,ownership,timestamps),
 if possible additional attributes: context, links, xattr, all

You can also use rsync.

sudo rsync -a /home/my_home/ /media/backup/my_home/

From the rsync manpage:

 -a, --archive
 This is equivalent to -rlptgoD. It is a quick way of saying you want
 recursion and want to preserve almost everything (with -H being a notable
 omission). The only exception to the above equivalence is when
 --files-from is specified, in which case -r is not implied.

 Note that -a does not preserve hardlinks, because finding multiply-linked
 files is expensive. You must separately specify -H.

See this question for a comparison between cp and rsync: https://stackoverflow.com/q/6339287/406686

Note the trailing slashes (see manpage for details).

cp -a

Where -a is short for --archive — basically it copies a directory exactly as it is; the files retain all their attributes, and symlinks are not dereferenced (-d).

From man cp:

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

I use cp -pdRx which will -p preserve mode, ownership & timestamps, -d preserve links (so you get symlinks instead the file contents copied), -R do it recursively and -x stay on one file system (only really useful if you're copying / or something with an active mount point).

PS: -R instead of -r is just habit from using ls -lR.

cp has an option to preserve file ownership. From the manual page of cp:

-p Cause cp to preserve the following attributes of each source file in the copy: modification
 time, access time, file flags, file mode, user ID, and group ID, as allowed by permissions.
 Access Control Lists (ACLs) and Extended Attributes (EAs), including resource forks, will also
 be preserved.

You can do something like this:

tar cf - my_home | (cd /media/backup; sudo tar xf - )

tar keeps permissions, ownership and directory structure intact, but converts everything into a stream of bytes. You run a "subshell" (the parenthesized commands) that change directory, and then get tar to reverse the conversion. A steam of bytes becomes directories and files with correct ownership and permissions.