I don't mind the alert or warning, but I do mind the weeks of having a blinking icon in my Menubar. Here's what I did in Terminal:
$ cd /System/Library/CoreServices/Menu\ Extras/Bluetooth.menu/Contents/Resources/
$ sudo cp lowbatt.pdf lowbatt.backup.pdf
$ sudo cp BlueTooth_Connected.pdf lowbatt.pdf
This replaces the low battery icon with the same connected icon. I assume the icon is still "blinking" in that it's switching one for the other, but since they're now the same, you don't notice.
Now I get the 20%, 10%, 5% alerts, but no annoying blink.
This is in Lion. It's likely that system updates and perhaps even Mountain Lion will undo this, but it can probably be reapplied after updates are performed.
For Mountain Lion, the relevant files are named:
How can you disable the low battery warnings for bluetooth devices? by seanhussey