There are a couple of computer programs available that can help.

• Track Designer was originally built by Matt Bates, but is now being maintained by the North Georgia Lego Train Club. It includes templates for road plates, plain baseplates, some train-related Lego sets, and train and monorail track. It requires Windows 95 or later to run. One disadvantage is that you cannot easily make text notes as to e.g. building locations: to do that you need to cut-and-paste the screen image into a paint program and add the text there, or print out the layout and write on it.
• LDraw is a system of tools for Computer Aided Design of Lego models. Various editors for different platforms exist, allowing you to lay out baseplates and move them around. Train track is not currently supported officially, and Track Designer is much easier to use for train track layout. Find the various LDraw tools at LDraw.org.

I've set up some pages of baseplate pictures which you can print out from your computer, color to match your available baseplates, and write on to your heart's content:
Plain baseplates
Road and Raised baseplates
Space, Runway and Raised baseplates

To use the paper cutouts, make an outline drawing of your available area at the same scale as the printouts (a standard 32x32 baseplate is 10" square), make photocopies of it, then start laying out the paper cutouts and moving them around. You can make several alternative arrangements and compare them, then pick the one you like best. Once you've fixed your design, you can place it in a page protector, laminate it, or permanently glue the pieces down to keep everything in place.

Next: Layout Design (coming Soon)