you can to with ntfsclone (man) for ntfs and ... well... tar for ext3 :)
i can really advise you using ntfsclone for ntfs, i am using it excessively, it's simple and efficient, quick and small, therefore well scriptable.
you can use tar to back-up and clone ext2/ext3 filesystems, but I'd rather suggest you using xfs, as it has enterprise-like backup software, called xfsdump, which can restore the XFS filesystem just as it was (with even security attributes too)
The way I am backing up my system (shell code snippets)
COMPRESS=pbzip2 -c
sudo xfsdump -p 30 -l 0 - /dev/sda1 | ${COMPRESS} | ccrypt -k /tmp/passfile -e > ${DEST}/${DATE}-root.xfsdump.bz2.ccrypt
dd if=/dev/sda of=${DEST}/${DATE}-mbr.dump bs=1 count=512
YMMV, but after a time I'm sure you will find xfsdump and ntfsdump very useful. The best thing they provide that both filesystem and filesystem content is saved in one step, both are command line utils, therefore it's easier to "script" them than gui-based competition, plus xfsdump creates a (shrinked) file format you can even loop-mount to inspect the contents.