Sometimes, before I embark on a really big project, the OCD part of me demands forethought and planning so that everything lines up just right. Usually, I use MS Excel. What I do is shrink the columns and rows to make a nice grid. Then, I change all the borders to a light grey, so that unused blocks will still print on paper. Then, I use black borders to mark where I'm building, and a fill color to denote block type. For the truly big and complex projects, I do a top-down view as well as a sideways view. I find this helps both with making everything meet up and even out, and it also helps me effectively manage my creative ideas.
What do you use to plot out your epic projects?