I was having the exact same problem with my Zune, except my battery never died. It was fully charged (or so I thought) before it stopped working.
However, I did manage to get it working. I hope this works for the others having a similar problem.
I kept my Zune on the wall charger, and while doing that I did a complete reset (hold down back + left + center while the device was booting up) and it deleted the firmware as well. Now, I don't know if that is completely necessary, but I'm just stating what I did. While the device was still on the wall charger, it wanted me to connect to a PC except, hey, cool, I can't because it would just flash on and off. So I just left it on the wall charger over night and for most of the day (must have been 20+ hours, since I had class)
Moving on. I unplugged the Zune from the wall charger, then plugged it into my PC. Still flashing. I don't know where I read this trick, but I put the device on lock, held down the back + center + play/pause button, and while holding those three keys down on the device, I unlocked it. It booted up normally, told me to connect to a PC (which it was) and it installed the drivers, then the firmware once I opened the Zune software.
I resynced all my music/movies with no troubles at all, and my Zune has been working as if nothing happened to begin with. Like I said, I hope this worked and good luck!
