I'm working on a 9v battery replacement using supercapacitors and one IC that I found nice specs wise was LT1613 :
http://www.farnell.com/datasheets/1605123.pdfIt's up to 90% efficiency, it can do 3.3v @ about 30mA (which should be enough for your needs) from a 1.5v battery and obviously much more with higher input voltage.
Considering you plan on using 3v batteries, which can usually do about 3mA of current, I guess your circuit doesn't use much power so other than being expensive, this IC would work just fine.
The datasheet also shows the regulator working in SEPIC configuration, so it could work with wide input voltage range, below and above 3.3v with no problems.
Just consider A CR2032 (3v battery) usually has about 200mAh while even a small 1.5v AAA alkaline battery has about 1200mAh. It would also take about the same space on pcb as two 3v batteries in battery holders.
Anyway, the only problem is that it's a VERY small chip.. I put it aside because i practically have to etch a pcb (and i don't have the chemicals at the moment) or order one just to make a prototype.
So I had a second look and found LT1307:
http://uk.farnell.com/linear-technology/lt1307cn8-pbf/ic-dc-dc-up-converter-1307-dip8/dp/9560394Here's the datasheet:
http://www.farnell.com/datasheets/25129.pdfThis is also available in DIP format, and works as low as 1v, but it's only about 70% efficient with low input voltage compared to the previous one... and it's still quite expensive.
But it would still be much better to do 1.5v aaa to 3.3v instead of 3v cr2032 to 3.3v
You might also want to check ISL9111 in fixed 3.3v output:
http://www.intersil.com/content/dam/Intersil/documents/fn76/fn7602.pdf Should do 3.3v with up to 80-95% efficiency with input voltages between 1.2 to 3.3v (this one's only boost, you don't want to give it more than 3.3v)