If you're in a large cavern or have hollowed out a mountain, try building a redstone-controlled light pillar in the center that glows according to the daylight signal strength. You could place the daylight sensor at the peak, and perhaps run the redstone down a spiral staircase, connecting lamps or lava dispensers along the way. This would allow you to hide the redstone within your build.
Make a big room called Main Hub, get some saplings and seeds, create a room called Farm Hub with stuff and tunnels that lead to farms, with animals and a bedroom and Crafting Hub, a furnance room, craft room, anvil room, armories and so on! Hope I helped
Have an underground garden, complete with grass, fake trees (not cobblestone, cobble trees are depressing), mushrooms and maybe an animal or two. Also I suggest adding a portal room, with cobwebs to annunciate the 'creepy' feel, maybe a doorbell (rigged up with a pressure plate and a noteblock) and traps, lots of traps. Oh and a prison. Just suggestions.
If you want to make it as secret as possible, then the entrance needs to be a piston door. There are dozens of different types of doors on Youtube, but here are a few devices shown by Mumbo Jumbo that may help: