Tree Farmer (Untested)

local settings = {
  saplings = 13,
  bonemeal = 14,
  fuel     = 15,
  sample   = 16
}

local function refuel()
  if turtle.getFuelLevel() > settings.min_fuel_level then return end
  for i=1, 12 do
    if turtle.getItemCount(i) ~= 0 then
      turtle.select(i)
      while turtle.getFuelLevel() < settings.min_fuel_level do
        turtle.refuel(1)
      end
      if turtle.getFuelLevel() > settings.min_fuel_level then return end
    end
  end
end

local function drop()
  if turtle.detect() then
    for i=1, 12 do
      turtle.select(i)
      if turtle.compareTo(settings.sapling) then
        turtle.transferTo(settings.sapling)
      end
      if turtle.compareTo(settings.fuel) then
        turtle.transferTo(settings.fuel)
      end
      turtle.drop()
    end
  end
end

local function usage()
  print("Usage: tree")
  print("")
  print("  Saplings: " .. settings.sapling)
  print("  Bonemeal: " .. settings.bonemeal)
  print("  Fuel:     " .. settings.fuel)
  print("  Sample:   " .. settings.sample)
end

if turtle.getItemCount(settings.saplings) ~= 0 then
  print("No Saplings")
  usage()
else if turtle.getItemCount(settings.sample) ~= 0 then
  print("No Sample")
  usage()
else
  while turtle.getItemCount(settings.saplings) ~= 0 do
    turtle.select(settings.sample)
    if turtle.compare() then
      turtle.select(1)
      turtle.dig()
      turtle.forward()
      local height = 0
      while turtle.detectUp() do
        if turtle.detect() then
          for i=1,4 do
            turtle.dig()
            turtle.turnLeft()
          end
        end
        turtle.digUp()
        if turtle.up() then height = height + 1 end
      end
      while height ~= 0 do
        if turtle.down() then height = height - 1 end
      end
      turtle.back()
      refuel()
      turtle.turnLeft()
      turtle.turnLeft()
      drop()
      turtle.turnLeft()
      turtle.turnLeft()
    else if turtle.detect() then
      turtle.select(settings.bonemeal)
      turtle.place()
    else
      turtle.select(settings.saplings)
      turtle.place()
      turtle.suck()
    end
  end
end