Microcontroller boards are getting smaller and especially in smaller ones those programming headers become annoying. Think of 6-pin AVR ISP header – even on Arduino board it can be in your way. If you need to program MCU, you cannot get rid of it. So many of hobbyists probably start making custom solutions in order to save space. Danny suggests to take a look at so called tag-connect solution, where connection can be made with spring loaded pogo-pins that are normally used for testing PCBs during manufacturing.
It seems that they can serve programming and debugging purposes on small boards pretty well. You can make easily make ISP to tag-connect adapter cable pretty easily and next time design PCB with much smaller ISP footprint. Using tag-connect you are not only saving on board space, but also you need less drill holes and don’t need pin header anymore.