If the Arduino seems to expensive for some projects you should treat it as an development platform and then change to a design that has only the necessary hardware. The minimum hardware can be build for under $10. Here you would design with the arduino and transplant the programmed chip when your design is ready. If you don't need serial communications you can build a clone on simple proto board
if you need serial communication and your pc has com ports and you can manufacture pcbs you can use the single sided arduino clone
if you can not manufacture pcbs the old non usb arduino pcb is still available from some vendors.
To do this you need to be able to program the boot loader into the Atmega chip that you will transplant. The Arduino Diecimila, Arduino NG and Arduino Duemilanove can do this through the FTDI USB to serial chip that they contain.
If you want to build an simple AVR programmer look at