Any wooden shelves, shelf supports, counter tops, or wood to support cupboards or lofts can be embedded into the cob as you build. It's much easier to sculpt cob around wood than to cut the wood later to the organic shape of the dry cob. Everything that you build in as you go will save you a lot of fussy wood cuts later. You may want to keep the wood clean by covering it with cloth or plastic while you build. The counter, loft, and sturdy shelves can serve as scaffolding. Make sure the cob has hardened enough to support the protruding wood with your weight on it before you stand on it.
If you choose to put your counter or loft in later, you can leave a little cob shelf (2 or 3 inches) to set it on.
To support something small like a counter or shelf, compensate by making the walls a little thicker below the ledge. For a loft, you might want to make the whole wall a little thicker from the foundation up. You can cut the counter (or floorboards) to fit and set it on the ledge. Fill any gaps between the counter and the wall with cob or plaster.
Counters may need extra 'legs' to support their outside edge. These can be made out of wood or you can build cob pillars. These can also support shelves under the counter. If you want to attach cupboard doors, bury in a piece of wood to attach the hinges to. Remember to add something to help key the wood to the cob.
For two-story houses, you can save space by burying pieces of wood for steps that protrude out from the walls into the room. The cob is very strong and can easily hold the wood in place. This stair system has been used for centuries but is not very safe for little kids and will not pass any building code.
Niches are recessed spaces built into walls to create an altar, bookcase or a place for candles. These are fun to sculpt in as you build. If you finish a wall and then wish you had built a niche, you can carve one out later. This is much easier to do if the cob is still wet.
If you bury colored bottles though the back wall of the candle or light fixture niches, you'll see the colored light shining through the walls when you're outdoors.
The tops of the niches can be treated like any other opening. They will need a lintel or an arch. If you make niches less than a foot wide, you can forget about the lintel or arch rule and let your imagination go.
The thinner walls in the back of the niche will be less insulating than the thicker parts of the wall. If you live where it's really cold, you may decide to forget the niche idea. Books are good insulation so you could make a bookcase niche and keep the shelves close together and full.