MCEdit is essentially the only true 3-D editor for Minecraft as of right now. It is a separate program that loads up one of your worlds for you to edit. This program can either be extremely efficient and rewarding or one of the most frustrating things that you will ever use. I highly recommend starting small in terms of construction in order to give yourself time to adjust to the controls.
I use this program quite frequently seeing as it allows you to place your spawn point anywhere you want as well as the current player location. Words cannot describe how nice it is to be able to basically relocate to wherever you want on the map. One feature, however, that always bugged me was the insane controls and lack of the ability to copy objects from one world and past them into another. All in all, it's an essential program for anyone who takes Minecraft art or construction very seriously and plans on making building and other objects in a large scale.
Note: This program is quite CPU intensive and "weak" computers might struggle on larger maps. Also, this program is still in a pseudo-testing phase and may affect your minecraft.jar file. Always remember to keep a spare copy of it somewhere on your computer.