I charge my PS3 controllers from the USB ports in the back of the Wii - they're still active even when the Wii is off, unlike the PS3 USB ports. I've noticed though that if I've got a SIXAXIS connected to the Wii and its fully charged (i.e. the blinking LEDs are off), when I turn the Wii on it starts to charge again.
Any ideas? I figure that maybe the Wii outputs more current to the USB ports when its turned on...