you can use the program called rsync to do the backup,a dn use the --exclude or --exclude-from parameter for the exclusions, with the exclude option you specify a particular file, ie --exclude=junkfile1, with the --exclude-from parameter you specify a file containing the name of files you want to exclude. For example:
I create a file in my home folder called exclude and type the lines
then I can type in the terminal
This will back up the folder but leave out the files in /home/$USER/exclude , you can inclde wildcards in the exclude file, for example to exclude all .txt files you would add a line in the file *.txt
rsync -auv --exclude-from=/home/$USER/exclude /directory/to/be/backed/up/ /media/USB_Stick
type in 'man rsync' in the terminal to get a full list of the options available to rsync.
EDIT: as the user above said you can also use the --include parameter