Measuring total energy used by a project
Charge up a cap to a known voltage.  Then power this circuit from the cap for whatever time period.  When done, measure the voltage left in the cap.  Change the size of the cap to whatever is appropriate for the power draw and length of the test.  Here's the formula:

\$Amps = Farads * \frac{(V_{start} - V_{End})}{Seconds} \$

The result, amps, will be the average amps for the duration of the test.  Remember that the cap is measured in Farads, so don't use microfarads instead.

The cap voltage drop during the test should be fairly small, maybe 0.1 or 0.2 volts.  Any larger and you get other weird effects influencing your measurements.

And another note:  Most caps have terrible tolerances on their capacity.  Calibrate first using a 1% or 0.1% resistor load instead of your micro-controller circuit.  Try to have your V_Start and V_End approximately close to what you'd have for the real test to maximize accuracy.  Oh, if you can avoid it, don't leave your multimeter attached for the duration of the test, only for measuring the start and end voltages.

That's the best thing I could think of for measuring very low power stuff over seconds or minutes.  If properly calibrated it should also be quite accurate.