For nuts, bones and shells you need an all our a small hand drill to create the hole to string through. Acorns, hazel nuts, small vertebrae and all poocka shells are all excellent examples. With a fine drill you can turn any of these into lovely beads. If you have bigger pieces of bone, stick, antler, or shell that you need to cut down, you may also need a fine toothed saw or a carving knife to make the smaller pieces you can then drill for beads. And perhaps a bit of sand paper to smooth them out. If you really get good with carving you can make shaped wooden and antler beads, although just making flat disks of beads is plenty awesome enough too.
Berries and seed pods need only be pierced with a blunt ended needle while they are fresh and put directly onto string to dry. You might want to move them around a bit every few days while they are drying so they don’t stick. Rowan, holly, elder, and hawthorn all make decent beads like this. You can also cut and dry pieces of leathery fruits like apple and dry them into beads.
The papery bark of birch and cedar can be rolled with glue into cylindrical beads. Some larger long petals can also be preserved into beads in this manner. Coat the bark or petal in glue and then roll it, set it out on plastic wrap or wax paper and let it dry.
Petals like rose petals can likewise be partially dried and minced up and then worked into a paste to roll into round beads, then pierce the balls with pins and let dry to create lovely scented beads.
For stones and harder bones, you need a dremmel to drill through them to create beads. Or if you find stones with natural holes in them, like holey-stones/hagstones, they make wonderful beads.
The lovely thing about making beads out of natural materials is they are excellent for prayer beads, charms, and witchy magic. Rowan on red thread is traditional for protection and travelling. A rowan prayer bead set would be great for counting as you go into trance for hedgecrossing. Hawthorn is often associated with the white faced goddess and the beads could be great in a devotional piece to her. Rose rosary beads are excellent for Mary Mother of Peace. Antler or Horn is excellent for many a god like Pan, Cernnunos, and Callieach. Oak and Acorns are great for Dagda, and Hazel for Brighid. A sea shell bead would be excellent for Aphrodite or Mannanan and sea witch magic. The list goes on. Be creative and have fun!