I have some SMD Atmega328s and bought some 10mm LEDs
EAGLE schematics file
sch - 562.55 kB - 05/08/2017 at 19:43
EAGLE board file
brd - 125.18 kB - 05/08/2017 at 19:43
The blue is still a bit too strong, even with a 1k resistor.. meh. (edit: progger runs on 5v, not the tested 3V3 :D )
checking resistor values. Yellow gets 100 ohms, blue 1k ohms.
As soon as I've had send the board, I just knew that new ideas would flood in. Here's a list of improvements for the board.
I've added a size mockup with some 10mm LEDs I still have from other projects. The ones I've bought for this project look more like this: