The latest PPAC layout has the DS1307 on the right side, with the battery holder on the bottom and interrupt going to A3; I would have tested the schematic on a breadboard tonight but I can't find any 10K resistors. I added an I2C EEPROM too (or, at least a socket for one-- I don't have the little sucker yet) for program settings, maybe a log of wake up times, and relief for the ATmega's built-in EEPROM.
Not to whine, but I'm getting impatient with EAGLE's autorouting for 1-layer boards-- I can usually find a route for the missed connections, and it's annoying to have to push around so many traces to fit them in. This board layout was routed completely by hand after EAGLE kept leaving at least four air wires. It might work as-is, or I may spread into the unused areas and widen the traces. Must resist the temptation to just etch it and build it before breadboarding the whole thing-- I want to have the program ready for this specific circuit, since I shuffled some pins around on the EAGLE layout after converting it from my previous working breadboard circuit.