This tutorial explains how to migrate from an Arduino board to a standalone microcontroller on a breadboard. It's similar to this tutorial, but uses an Arduino board to program the ATmega on the breadboard.
Unless you choose to use the minimal configuration described at the end of this tutorial, you'll need four components (besides the Arduino, ATmega328, and breadboard):
Burning the Bootloader
If you have a new ATmega328 (or ATmega168), you'll need to burn the bootloader onto it. You can do this using an Arduino board as an in-system program (ISP). If the microcontroller already has the bootloader on it (e.g. because you took it out of an Arduino board or ordered an already-bootloaded ATmega), you can skip this section.
To burn the bootloader, follow these steps:
You should only need to burn the bootloader once. After you've done so, you can remove the jumper wires connected to pins 10, 11, 12, and 13 of the Arduino board.
Using an Arduino board to burn the bootloader onto an ATmega on a breadboard.
Once your ATmega328p has the Arduino bootloader on it, you can upload programs to it using the USB-to-serial convertor (FTDI chip) on an Arduino board. To do, you remove the microcontroller from the Arduino board so the FTDI chip can talk to the microcontroller on the breadboard instead. The diagram at right shows how to connect the RX and TX lines from the Arduino board to the ATmega on the breadboard. To program the microcontroller, select "Arduino Duemilanove or Nano w/ ATmega328" from the the Tools > Board menu (or "ATmega328 on a breadboard (8 MHz internal clock)" if you're using the minimal configuration described below). Then upload as usual.
Uploading sketches to an ATmega on a breadboard. Remember to remove the microcontroller from the Arduino board!
If you don't have the extra 16 MHz crystal and 18-22 picofarad capacitors used in the above examples, you can configure the ATmega328 to use its internal 8 MHz RC oscillator as a clock source instead. (You don't really need the 10K pullup resistor on the reset pin either, so we remove it to get a truly minimal configuration.)
You'll need to install support for an additional hardware configuration:
Once you've done this, you can burn the bootloader and upload programs onto your ATmega328 as described above. Be sure to select "ATmega328 on a breadboard (8 MHz internal clock)" when burning the bootloader. (If you select the wrong item and configure the microcontroller to use an external clock, it won't work unless you connect one.)
This procedure works on Arduino 1.0.x software.
Using an Arduino board to burn the bootloader onto an ATmega on a breadboard (w/o an external clock).
Uploading sketches to an ATmega on a breadboard.
Once you've programmed the ATmega on the breadboard, you can eliminate the Arduino. To do so, you'll need to provide an alternative power supply for the microcontroller. See the standalone Arduino on a breadboard tutorial for details.