Choosing a Switchmode Converter for a Battery Powered Project
If simplicity is a key goal, an integrated voltage doubler such as the ICL7660 or MAX1044 would work well:



Two capacitors, 2 diodes, and it's done. 

For the two diodes shown in the schematic, Schottky diodes with forward voltage of 0.35 Volts or lower would result in output voltages of:


For fresh batteries: 2 x (1.5 x 2) - 2 x 0.35 = 5.3 Volts
For depleted batteries: 2 x (1.3 x 2) - 2 x 0.35 = 4.5 Volts


Both are within the DS1307 supply range.

Examples of suitable Schottky diodes: 


Vishay VS-95SQ015, through-hole, but overkill and expensive
NXP RB521CS30L, Leadless SMD (SOD882) but inexpensive, with great specifications