I have now designed a PCB which is meant to cover all my clocks, past and future. 

It has an ATMEL328P chip (internal clock) and a RTC chip with crystal and battery backup, a stepper driver,  5V regulator (optional, solderbridge to bypass).  and a 3way button on the edge for setting time. Last but not at least plenty of pin holes for connecting things, stepper, and/or 2 servo, 2 digital IO, one analog, Serial for programming or debugging and the standard ICSP.

For this clock, the Stepperdriver part will not be populated, and the barrel connector will use 5V and no regulator either.

Of course, I still have to solve the mechanical problems I have.