When low power consumption is important, you have to look at the whole picture. A microcontroller with low Joules/cycle is only one thing to look at.
A good start would be to pick a battery and micro combination where the micro can run directly from the battery over the useful voltage range of the battery. Many PIC microcontroller, for example, can run from 1.8 or 2.0 V up to 5.5 V. That nicely covers a single lithium ion cell, two or three primary "1.5 V" cells in series, etc.
Another important strategy is to let the micro sleep as much as possible. If you only need to check something once a second, then maybe you can have the micro wake up for 1 ms every second. That means you need to look at sleep current carefully. It also means you want one with a built-in RC oscillator to minimize startup time, assuming a few percent clock rate accuracy is good enough. There are lots of tradeoffs.
You didn't give enough information to have some idea of the computing power required, so we can't say what would be adequate. But in general, take a look at any Microchip PIC with the "XLP" (extra low power) feature. In particular the 16F1xxx series has some impressively low power devices.