You can:
use it for the back of a lap quilt, the flannel will make it cling
mix it with denim patches or back a denim quilt
make a primitive-style top
use it for raw-edged applique
line a garment for warmth
stitch cozy pillowcases
use it like regular cotton goods in a quilt top
layer for pot holders
make needle books
check with local charities for layette/crib quilt needs
add inside cuffs/collar to a sweatshirt
construct penny rug type table topper
Google "flannel crafts" or "flannel quilt" for lots of inspiration.