The GameCube was Nintendo's so-called "darkest hour" and even then they were profiting. This is a company that has been around for more than 100 years and in the few short decades that it has been a video game company it's always made a profit. Nintendo has NEVER been in trouble, ever... the closest they've been to DOOM is during World War II for obvious reasons.
All this "Nintendo is doomed" talk happens all the time and I don't really understand it.
To put things into perspective, out of the big three console manufacturers, they're the only ones to profit from making consoles. That and they're a company that has 0 debt and a lot of money in reserve.