Take a circuit that you know reasonably well, design it in Eagle PCB or Express PCB.

Make a schematic file, make a board file

This will get you through the process of inputting your circuit design into the computer.

Eagle Circuit Board

Once you have a schematic, you will need to make a board image. It makes a certain amount of sense to start with a layout that is pretty similar to the schematic.

EtchingCircuitBoard:

print the board file, you can use ferric chloride to remove the unneeded copper, leaving just the connections you need.

Milled pcb

make the board file, send to micromill, remove unneeded copper, leaving just the connections you need.

PrintedCircuitBoards has a few ways to make your own circuit board.

Here is some info on Eagle:

http://www.instructables.com/id/EZ3WN1QUKYES9J5X48/?ALLSTEPS

http://www.instructables.com/id/EN4JHYI8R7EYF7IYHZ/?ALLSTEPS

http://www.instructables.com/id/E65LY13F03FMNR9/?ALLSTEPS

a sample file - http://electricity.pbwiki.com/f/motorcontroller.zip

eagle to g code - http://www.brusselsprout.org/PCB-Routing/

here are some other links

http://falstad.com/circuit/ has some great visualizations

CadCircuits

Here is some info on Eagle:

here are some other links