I've created an RTC Breakout for DS1339 on Arduino, including a library for the module. Here is the instructable that I published -
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!
I've finally gone ahead and created a fully assembled breakout board with the DS1339 RTC with smd components and created a double-header, so you can use it by plugging it directly into an Arduino or a Raspberry Pi - as the board is tolerant of 3.3 and 5v.
It is available on Tindie if you are interested! - https://www.tindie.com/products/UpbeatLabs/ds1339-rtc-breakout-board/