Electronic – How to implement an ISP connector on the board

I've used ISP for just about every AVR board I've done; it's nothing to be afraid of. The AVR ISP mkII manual gives a pretty good summary of the limitations you need to look out for in the "Target Interface" section. Basically, if you run the MISO/MOSI/SCK pins directly to the programmer and have about 820 ohms between them and the rest of the circuit (and aren't doing anything funky with the reset pin) you're okay. I wouldn't worry about the ISP damaging other components; it's not a high voltage programmer. The signals all run at 5V, so if it can damage an external component, so can your microcontroller.

If you're really stuck with a board that doesn't permit ISP programming, I'd at least try to use a ZIF socket for your programming board. They're pricey, but it will greatly improve your quality of life.

First, you have identified a really annoying part of SPI on the AVR: Connecting SPI slaves will interfere with the proper operation of ICSP.

Second: The SPI bus has MISO, MOSI, and a chip select pin. You can break out the MISO, MOSI and GND pins, and perhaps VCC, plus a different CS pin for each daughter board you want to connect. As long as the CS is not active for the daughter boards, and the daughter board chips do not try to use the bus in master mode, you should be OK.

Third: You can use a buffer chip of some sort (perhaps 74HC125 or similar) with a tri-state function to isolate the ICSP feature from the SPI-talking-to-slaves feature; set the buffer chip up to require a particular pin high to let signals through, and use software to pull that pin high only when your code wants to talk to the slaves, and keep it low after a code reset.