Let me tell you about my mine.
At the top of a hill, I built a cobblestone tower of 4 a side, 2x2 hollow inside, with the second layer from the bottom made of glass for vision. Above about five blocks the tower is dirt, since creepers can't make it up that high and I ran out of cobblestone. A diagonal tunnel inside the tower leads down as far as bedrock. The tunnel is five high, minus one for stairs, and lit by torches.
At the base of the tunnel it branches left and right. This is the main tunnel. Mining tunnels are dug every four blocks along the main tunnel on both sides. To prevent getting lost, the main tunnel has cobblestone floor and roof. A redstone torch is placed on the floor at the stairway.
A vertical shaft near the stairway leads upward. The pattern is repeated on every level, except that the mining tunnels are shifted along by two. This setup makes more blocks visible. The mining tunnels having three blocks between them means there's one row which isn't seen from the tunnel on either side, but you only miss seams that are no wider than one block and no higher than two blocks, so its' not that big a loss.
Up top, I realized I left no room for chests and built them outside. Then I used the stone to build a wall around it. This still left me vulnerable to arrows and creepers exploding my chests, so I built a great wall around the whole area and filled it with saplings and torches. I put a viewing platform on top of the tower and noticed it was within sight of my original base. Distinctive towers are useful landmarks.