So I found this mountain that's like a natural fortress (with a little help from me anyway).
I decided to build a comfortable bungalow on top, along with a small garden and some crops.
To keep this little eagle's nest safe from (imaginary) invaders, I made sure the only way to get to it is through a series of underground shafts and tunnels that lead to discreet doors at the base of the mountain.
From that point, you can also get to a secret exit behind a waterfall or straight down to the bedrock through a mineshaft.

This is a modest project, of course. The goal is to blend in the existing nature and make you at home without being easily noticed from anyone.

Notes:
- All of this is hand made. The only non-legit aspect is that I have used Minutor to locate resources and dungeons and used MCEdit once to create an oversized glowstone crystal in the Glowing Cave.
- Unless you turn on fancy graphics, clouds will wander through the bungalow. Sorry about that.
- None of this has been tested with aggressive mobs on. None of the shelters are mob proof.

Version 2

The base concept has evolved in the following way:
In the basement of the house, a portal leads to the Nether, where a series of secure walkways lead to other portals, which in turn give access to remote places in the outer world. Those outposts are not easily spotted and are excellent lookout posts to check for invaders.
In the Nether, a Ghast observation chamber was also added, so that when you turn on mobs some ghasts will probably wander just a few meters from your head.

Version 3

Version 3 features an additional 3 portals.
- The first one leads to a shelter deep under the earth, next to a hole in the bedrock layer. So if you'd like to jump out of the world, be my guest.
- The other two portals can be reached through a new railway system in the Nether. They link to interesting far away places that remain unexplored.
At the end of the railway you'll also find a medium sized Nether cavern that contains several glowstone formations, including an oversized one hanging from the ceiling.

Texture pack used in screenshots and video: johnsmith_V7
www.minecraftforum.net/viewtopic.php?f=25&t=29164

As of Minecraft version 1.4, this texture pack still requires the HD texture fix to be applied. Get it here:
www.minecraftforum.net/viewtopic.php?t=46173

Notes:
- Version 2 features an easter egg hidden somewhere in the Nether. You could go and look for it. The walkthrough video may give you a tiny hint at where to start. ;)
- Custom texture pack is not required.