Wood and charcoal are straightforward -- harvesting a tree gives you wood and saplings, saplings grow into trees, and wood can be cooked in a furnace to make charcoal (you can even use saplings, more wood, or more charcoal as fuel.)
If you make a 2x2 depression in the ground and put water in opposite corners, the remaining corners will immediately fill. You can then pull water out of any corner, and it will immediately refill.
Cobblestone can be generated by making water and lava flows touch.