I've created an RTC Breakout for DS1339 on Arduino, including a library for the module. Here is the instructable that I published - http://www.instructables.com/id/RTC-Breakout-for-DS1339-on-Arduino-low-cost-batter/
I was looking for suitable replacement for the DS1307, which is not suitable for a 3.3v Arduino Pro Mini. I settled on the DS1339, which had all the features I was looking for:
1) Tolerant of a wide range of voltages 2) Battery backup 3) 2 alarms, so you can use this module to wake up your arduino periodically if you have any low power projects as an added bonus, it has a trickle charger too!
I forked the Mosquino RTC DS1337 library (since the register formats are almost identical), made it more generic, and put it on github - https://github.com/sridharrajagopal/DSRTCLib
The board itself is available on https://www.oshpark.com/shared_projects/A21xcMiD
Hope this is useful to you! Cheers, Sridhar