This guy runs a Techshop Workshop for making end grain cutting boards, and having taken his workshop I highly recommend it:
WKS100: Two-Tone, End-Grain Cutting Board Workshop
This instructable should act simply as a supplement to his instructable. As a newcomer to end-grain cutting board making I made a few mistakes and observations that should hopefully make anyone else willing to tackle this project even more informed and prepared.
Full Discloser: I made it at Techshop and I highly recommend anyone near one to check them out.
Some nice pieces of wood (the cutting boards you'll see here are made with maple and cherry)
Glue: I used Titebond II. Just make sure it's food safe and will hold up ok when wet.
Lots of sandpaper
Heat gun (not necessary unless in cold environment)
Step 1: Design and First Cut
CBdesigner is the tool that is awesome for taking the headache out of checkered end grain cutting boards. I would highly suggest fully mocking up your design in this program before buying a single piece of wood. It will save you a lot of hassle. Here you can see the design I was shooting for.
2. Cut the first set on the table saw
Word of advice: be absolutely meticulous with your table saw cuts. I made the mistake of applying too much pressure against the fence, which pressed the wood against the blade, which meant that I cut away more material than desired. This ended up creating small gaps when I fitted the pieces together, which I was luckily about to close when I glued it all together. More on that in the next step.