Would you please be a bit more specific with your problem as I too have just suffered an error message with my Wind Waker. It may be a bad batch of discs.
Here's the specifics behind mine:
I have not had any problems playing my GCN for 15 months. I've played through about 20 games with no problems (other than the occasional Metroid Freeze).
My FIRST Wind Waker disc looked ok, but the system would not read it. It took about 5-10 minutes of fiddling with the disc to get the system to finally recognize. Once the system did read it though, it played fine for two 4 hours sessions.
Not wanting to go through the hassel every time I played the game, I exchanged it for a second disc (from a different store in the same chain).
The NEW disc was recognized and loaded with no problems at all BUT after playing for about 2 hours (right before the Dragon's Roost Boss fight), the game started to have trouble at load points. I would get a message along the lines of "Cannot read disc". Simply opening and closing the cover though would generally be enough to get the game back on track (it continued from exactly the point at which the error occured). Finally I got a "Power DOwn your GCN" message.
I did shut the system down for about and hour, and tried again. After 15 minutes of play (as the boss levels were loading), the system ran into the same problems all over again.
So my question is: Is this the game, the disc, or the system?
I would think that, if the fault lie in either the game or the system, that the error should be the same for each disc. But its not. Each disc had distictly different errors. These problems were consistently unique to that disc. (I haven't had the chance to extensively test other games but they do seem to be working fine). That would lead me to believe that the flaw lie in the discs themselves, but I am not much of a tech head, and I do have trouble thinking that I would crap out twice on the same game when there have not been any reports of similar problems.