What I/O are you using? without some basic specs it would be hard to say. Are you using analog inputs? PWM outputs? Serial? How many digital inputs? How many Digital outputs? Are you planning on making them permanent or will you reuse the parts?
Get a few blank 328P chips and learn how to load a bootloader or using your Arduino as an ISP learn how to program using the ISP option (no bootloader).
Look at the specs for the ATMega8 or ATtiny2313 and see how they might work for your application.