How to Make (Almost) Any PCB
1. Design your schematic
You can get Eagle, a free PCB design software suite, from the CadSoft website. There is an excellent tutorial for using Eagle here. I'll cover the basics of this process, but you should refer to that link for all of the details. If you need to make a new part, refer to the tutorial. Also check out the SparkFun Eagle tutorials: schematics, PCB layout, creating new parts.
You can make a schematic by adding and connecting parts in Eagle. Here's an Eagle library with most of the parts we use: fab.lbr (also see Neil's Eagle library). You should connect parts using the Net tool (and not the Wire tool).
2. Layout the board
Once your schematic is complete, hit the Schematic to Board button in Eagle, and the parts with connections will be automatically generated. After this, if you change something in your schematic, the board will automatically be updated as long as you have them both open at the same time.
To layout the board, you first place the parts and then place the routes to connect the parts. You want to place the parts so that you minimize the crossovers between the yellow ratnest lines. Before you start routing, you should hit the Change button and adjust your trace width to .012. Also, you should change the grid spacing (View -> Grid) to Finest.
If you have trouble routing everything, you can add a 1206 0 ohm resistor on the net to create a jumper. Also, you can route through unused microcontroller pins, just be sure to set them as inputs in your code.
Load this DRC rule file into the DRC checker to check the minimum distance between your wires. This is calibrated pretty well for the machines, but you should always visually inspect the toolpath before sending it to the machine.
3. Export the board as an image
Once you have finished the board, go to File -> Export -> Image. Check Monochrome and change the resolution to 500. Save the image as a PNG file. For detailed instructions, see the tutorial on exporting PCBs from Eagle for cad.py.
4. Machine the board
a) Modela
A more lengthy tutorial on the Modela can be found here.
Use the 1/64 end mill and set the Z height of the Modela.
Open the PNG file in CAD. Set xmin = 1, ymin = 1, zmin = -.005, and zmax = .05
Set the number of contours to 1 and check that none of your traces will be shorted. If they are, you can just edit them in GIMP.
Set the actual number of contours (to save time you can just do 3-5), and hit Send to Machine.
b) Vinylcutter
A lengthier tutorial on PCBs on the vinylcutter can be found here.
Load a piece of the copper roll into the Vinylcutter.
Open the PNG file in CAD. Usually the default force values work well. Hit Send to Machine.
Once the job finishes, take your piece out and trim the excess copper. Put masking tape on the copper side and remove the paper backing. Place the sticky side of the copper down on whatever base you are using. Press down the copper everywhere (you should go over it a lot with a credit card, the back of tweezers, the side of scissors, etc for a while) because the glue is activated by pressure. Pull off the masking tape without removing any copper, then you can begin to weed the circuit by using tweezers to pull off unwanted copper.
5. Stuff the board
Solder on all of your parts. The easiest way to solder surface mount parts is to put solder on one of the pads, and then re-heat the solder while holding your part in place with tweezers. Once this solder cools, you can let go of the part and solder the other pins. Then, you should go back and solder the first pin to make sure there is a good connection.
For parts with very small pins (like the mega88), you can put solder on all of the pins without caring about shorting, and then use the gold braid to remove the excess solder. You should be able to use the gold braid to remove all of the shorts and end up with a perfectly soldered part.
Tips and Tricks
Modela vs. Vinylcutter
Once you get the hang of weeding the vinylcutter, you can make boards from both of these machines in about the same amount of time.
The Vinylcutter is nice because the actual machining time is relatively quick, so it's not usually backed up like the Modela. Also, if you are making a large circuit, the Vinylcutter is the way to go unless you want to wait forever. If you do use the Vinylcutter, make sure you hot glue down the MTA connectors (after you have made sure they were soldered correctly!) or they will pull off when you try to take out the cables.
The Modela is good for debugging and making more reliable circuits. It is easy to remove/add/re-solder on Modela boards because they are pretty sturdy. If you try to do this on a Vinylcut board, you will probably pull off some traces accidentally. The Modela is also good if you have parts with small pins (like the mega88), because these are difficult to weed from the Vinylcutter. To reduce the machine time for the Modela, you can set the number of contours to a lower number (3-5) instead of doing the max number of contours (-1).
If you need to edit your circuit, but don't want to go through the hassle of changing it within Eagle, you can edit it with GIMP. Just add black or white depending on whether you want to delete or add a trace. When you save the file, make sure you do Save as... and check save resolution, otherwise the machines won't be able to read the file (it will open in CAD, but when you hit send to machine, nothing will happen).