This video shows a pretty decent method of planning out structures:
http://www.youtube.com/watch?v=fETsa9kewdIAlternatively you can do it oldschool and draw it out on graph paper instead.
There are other purpose built 3D minecraft programs out there but I think you'd gain more satisfaction from developing a build yourself from some basic floor plans and side/front elevation drawings.
If you don't care for the designing in an image editor then this might be for you:
http://minecraftstructureplanner.com/index.php/screenshots/application/3d-projection/I used this once for a build and it's not bad, sucks up memory if I remember correctly though. Bonus/negative (depending on which way you look at it) of this is that you can see what the build will look like once you're done.
However, as I said before, I think you'll get more out of the building side of things if you plan it using graph paper/grid image editing.