According to this report (in Japanese) there could be some issues with the PS3's new wireless controllers.

that is because the controller will have to be paired to the console via the USB cable before play. This pairing process will be required each time the console has been shut down and turned back on, or - given the rough translation - possibly every time the controller has lost power.

However, it doesn't appear that going into standby mode will cause the same issues.

Oh, and if you were wondering about battery life, it appears the controller is expected to get about 30 hours of playtime out of one 2.5 hour charge. On the downside, the batteries don't appear to be replacable so when they start not holding a charge the controller will likely have to get sent in for repair.