The only programmers I own are the USBtiny and a jtagmkII. The USBtiny won't work with devices having 64K or more flash and the avrjtagmkII isn't supported by the IDE out of the box. So I added the following lines to my Programmers.txt file:
jtagmkII.name=AVR JTAGMKII jtagmkII.communication=usb jtagmkII.protocol=jtagmkII
Actually you can add ANY programmer that is supported by AVRdude this way! Read the AVRdude help file to find the correct "communication" and "protocol" values for any other programmer.