You can use matching or contrasting color thread, depending if you want to emphasize the line or not. Usually I try to blend with the background pieces.
Here is an entire quilt where you can see the additional line added by the contrasting hand stitching. The striped look around the flowers is black crochet thread that was used to attach both both the outer white and the inner black portions of the petals. The same for the centers of the leaves, which remind me of coleus.
BTW, this quilt was a lesson in value using only gray, black and white fabrics. For a bit of rebellion and surprise, look what I did on the back:
You can see that I added a lot of hidden picture shapes while machine-quilting. Do you see a cat, bird, fish, and pine tree? Lots of fun!
And here is the weirdest quilt I have made in a Pamela Allen class: The Green Man. It took a long time to stitch down all his leafy parts by hand. Come to think of it, he was a fore-runner of the Cubist experiments from the current class, wasn't he? Look at those eyes!
And yes, leaving the fabric edge raw does sometimes give a frayed edge, but often that is desired in an art quilt. Bark, leaves, hair, all lend themselves to this technique.