These instructions are the steps we followed for a 2012 Honda Civic. Most Hondas should function in a similar fashion, but most newer ones should not require these modifications. When in doubt, contact your local mechanic.
1. Force Battery Charging
First, we need to make sure it stays charged. For this part, we just place a piece of plastic (or cardboard) over the light sensor in the middle of the dash, and duck tape it in place! This model honda (specifically the 2012 civic), has a dual-mode charging system [pdf] which allows it to drop into a lower charging mode to conserve power. It does this by detecting the electrical load and other conditions in the car.
The best way to trigger the battery to charge fully is to force the headlights to be on all the time, since that’ll cause enough power draw to force the high charging mode. also: see here and here
Important Note: After doing this, ensure your Honda has the headlight switch set to “AUTO” to allow the lights to automatically turn on and off with the vehicle. Since we covered the light sensor, they’ll always be on. Additionally, we set the headlight delay to off so they’ll turn off immediately after turning off the vehicle.
2. New Battery
We replaced the stock sized battery with an Autocraft Gold 85-2 battery. With the larger battery, the car now has a little bit more capacity and is less likely to die. With some minor adjustments to the battery bracket (we purchased this one at autozone) and some 1/2 inch rubber on the bottom of the battery holder as a shim to make the tray flat, we were able to fit the larger 85-2 battery in place of the stock one.
This step may not stricty necessary, and you may be able to get by just doing step #1. Since the problems with the battery mostly occurred during the winter months, we opted to do this as well.
3. Results
Since applying this, we have had no instances where the battery either dies or runs low. This seems to be the least destructive method to fix this problem, which seems to be wide spread with these kinds of hondas. Some other methods to solve this problem involve destructively modifying the ECM.