My problem was I wanted to take an Arduino prototype and make it a Production project. I did a lot of Googling for how to take an Arduino project to Production. I could not however find anything about how people took a simple Arduino project and made it into something standalone. After a while I started reading a lot about Atmega328 (The chip on the Arduino) and ran across a post for a Standalone Arduino on a breadboard. From there I came up with my own process that allows me to prototype with my Uno, then take it to the next level. I can do this very quickly now with just a few parts.
The first thing I wanted to do was to be able to pull the chip off. You can get a cheap IC Extractor from Amazon.com. I personally don't suggest that you make this the regular practice if you are going to program a Atmega328 and put it into your projects. I suggest you get yourself a 28 pin ZIF Socket. I did buy this one from Sparkfun only because I was ordering other things. You can find them cheaper on eBay but this is only $3. Then once you pull off your Atmega328 from your Arduino Uno, carefully push in the ZIF socket. You'll notice that there is just barely enough room for it on the board, but if you are careful you can insert it. Then you can swap in and out as many Atmega328's as you want.
You can see here that once you do this, you'll be able to quickly swap out the CPU. Be very careful when you press this into the socket. It is a very tight fit. You also have to be careful not to press too hard since it does cover the small can on the left.. So with a little effort you can now program the chip and use it in your project. Using the whole Arduino is complete overkill for your project. With this Standalone Arduino instructable you'll see you only need a couple of capacitors and a crystal. I was able to order them from Sparkfun with the Uno Bootloader already on the Atmega328. From there, you can breadboard your project. If you need to change the code on the chip, with the ZIF socket, its easy as cake to swap it in and out.
Then I was able to find this excellent reference to the pins for the Atmega with the Arduino bootloader on it. So, if you read this whole article you can see that if you read a few web pages, and buy a few parts you can take your chip off your Arduino and place it into its own production board. The extra parts will cost you about $5 and a new Atmega328 with the Arduino Bootloader on it about $5. What that means is that you can create production projects for about $10 each. That's less than 1/2 the price of buying an Arduino Uno for each project you create.