Electrical – Driving a 5V IR led with a 5V charger

The amount of light LEDs put out has a very linear relationship with the current they are driven with, and the voltage to current graph is relatively constant as they are diodes with a characteristic junction voltage. Taken together, this means that the efficiency can rise about 25% if an LED is driven at 10% of rated brightness (in this LED, but others should be fairly similar).

In any case, regardless of the level you choose to drive the LED at, what you want is a "single cell LED driver". These are usually current-regulated, eliminating the need for any resistors which do nothing for your efficiency, and also have the ability to step-up the voltage, so you can drive a 3 V nominal LED with one or two 1.2 V NiMH cells.

Linear, Micrel, and Diodes Inc all make drivers for this purpose, and you can find many more in a search for "single cell LED driver".

Your circuit is fine. It's the same circuit which is used in hundreds of millions of commercial remote controls, and they operate for at least 15~20 years. You could use a series resistor (and place LEDs parallel), but you'll decrease the operating range.

In case you want to use the RC-5 protocol: the old remote controls used a 50% duty cycle for the modulation. With the use of microcontrollers that has been reduced to 33% or even 25%. Neither is a problem for the AVR. Shorter duty cycles make your batteries last longer.