I just wanted to announce that I've created a KiCad library of AVR microcontrollers with the Arduino pinout (https://github.com/ppelleti/avr-arduino-kicad). The schematic symbols are marked with the Arduino pin numbers (D0, D1, … and A0, A1, …) in addition to the AVR pin names. This should make it easier when designing boards that are meant to be programmed with the Arduino tools. (In other words, a "breadboard Arduino", except that you're making a custom PCB for it.)
The library has symbols for 8-pin, 14-pin, 28-pin, and 40-pin DIP AVRs. It also has symbols for 6-pin and 10-pin ISP headers, and the 6-pin "FTDI" (serial) header.
The repository also contains templates for each size of AVR, with the minimal circuit necessary to make the AVR work.