Never done this before, so I ask… How do I specify that a small number of pads (for an ICSP connector) should be gold plated?
Ah… I just tell them that pads in positions xxx should be plated?
Or can I just add an extra layer/file just for those pads?
This is not enough. These pins should be connected together for electrochemical (selective coverage) plating. This connection after plating should be cutted off, so you have to place this connector near the edge.
Take a look a this tutorial: http://www.eurocircuits.com/blog/40-Gold-plating-for-edge-connectors
I think it’s better to gold plate the entire board chemically. The cost shouldn’t be too expensive.
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if gold finish is for connectors:
Electroplated gold is thicker and harder making it ideal for edge-connector contacts for PCBs which will be repeatedly plugged in and removed.
@keruseykaryu thanx for the useful link
Yeah, thx the for the link @keruseykaryu
@OP, make sure the boardhouse you choose accepts READMEs before you hire them.
Yes, PCBWing does. I have mailed them and asked. Note that this connector is just for reprogramming. it will not be used repeatedly.
Then ENIG will probably do, or just HASL if you’re not in a tropic climate or expect your board to be field serviceable 10 years down the road 
When you do boards för sockets for production test of chips where the pogo pins will grind at the pcb you specifically ask for “hard gold”
Don’t ask me what it is exactly.
I just ask for it.
True, perhaps I am overengineering it 
Just thought a dash of gold would look neat
I usually go ENIG, but I never imagined that you can go different finish in the same PCB. Nice!