For relatively small (less number of pins than ATmega328) projects, ATtiny series, ATtiny45 or Attiny85 are good choice in terms of its physical size (8-DIP or 8-SOIC) and low power consumption.
There are many ways to program it. One of the popular device is USBtinyISP
. Both of them work very well with WinAVR
I'd like to share how I program ATtiny85 with JeonLab mini 1.3
. The idea has been adapted from High-Low Tech Group
. One missing note from High-Low Tech Group
is that you need to add a 110-120 ohm resistor between VCC and Reset pins of JeonLab mini (or Arduino) to prevent Auto reset on serial connection as explained in here