Well, no company is invincible. In fact, when they're at their highest success is typically when a company loses their way and drives a few hefty nails into their own coffin. That said, I think that the company most likely to kill Nintendo--would be Nintendo.
Now, I'm not saying it's going to happen. Nintendo has routinely been recognized for their extremely smart business practices over the years. Even during the GameCube era, and if they can be recognized for their smart business practices during that, then they clearly know how to run a business.
The reason I go with Nintendo as their primary threat is because it seems rare for a company to just be killed by another. Competition with other companies may make things stressful, but it's ultimately the decisions of the company (we're talking about, I guess, Nintendo) that determine it's future.
Look at WorldCom or Enron or those over-large conglomerates. They killed themselves. And ultimately, in the world of video games, Atari and Sega killed themselves (where console manufacterers are concerned). In fact, internal decisions at Atari so violated every facet of that company that it can hardly be considered the same company these days. It's there in name alone; after so many mergers, sales, buy-outs, and changes in management.
Sega followed the other idea I laid out--that they were at the top of their game, and then fucked everything up. Instead of handling competition from the SNES smoothly, they went bonkers and thrust the Sega CD and 32X on the market, which only served to drive gamers further from the Genesis. Eventually, this led to enough bad decsions that the Saturn was launched early--pissing off just about everybody, and then they gradually lost more fan support, more third party support, and eventually money.
Nintendo's biggest threat is easily Nintendo. Luckily, they seem to be doing okay.