I padded a box I made with a material I found at Hobby Lobby. I just walked around thier fabric department till I found something plush without a print and went with that. I worked out fine, but I also put a backer of chipboard under the fabric to prevent any movement and/or wrinkles.
I would probably use a soft foam and covered it in a fabric for holding the glass ornaments. I have seen it fabric and craft stores. You can get various thicknesses, I have seen 1/2 inch up to 3 inches. It is like what is inside of a couch cushion. I think you could cut some indents in the foam to help hold the ornament.
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