I have been using a program that allows me a top down view of a base, but the program is very, very limited, and I just build simple buildings.
One thing I like doing is building towers, I used to hunt the wasteland and just use the natural terrain, but then decided to make my own hunting stands.
I learned the hard way, that a 1x1 tower of cobblestone can (and will) be brought down quickly.
I then upgraded to a 2x2 tower, and this worked and allowed for repairs and storage on top, so building materials can be left in a box up top. Attract and kill Bears and wolves, grab building materials from the local storage, hop down and make repairs, grab loot, and head back up top and store loot in the rest of the storage boxes. Rinse and repeat.
For building any building that you intend to keep long term, I would not build anything less than 6x6, and mostly use 9x9 construction.
If you like building a base with many above ground walkways, I would recommend a 3x3 ladder tower, with a least a two block wide ladder up two sides, and then connect your walkways together, using at least cobblestone blocks. I forget the name of the shape, but is the second shape in the basic menu, hollow/see through, so that you can stand on your walkways and see any pesky zombies that drop by, and eliminate them without having to go all the way down to ground level. Then just build higher and higher.
I really wish TFP would come up with a 'base planner' program, so folks could use it to show, real, in-game base designs and share them on the net.
