My opinions on what you wrote:
#5: Staying Young: I think this has hurt them. I don't think it would have had the impact it did alone, but I do think it hurt them. Even if there ARE a myriad of "older" games as mentioned in this thread, their marketing in general has NOT reflected that IMO. Their advertisements seem to still reflect the "younger" focus. Really the generational problem where those 40-50+ "in general" consider video games "for kids", and thus I think that attitude is more prevalent than it should be. This may also be a partial reflection on the almost-gertitocracy that Japan is. There may be many young minds there, but they aren't the ones making the decisions, and neither do they have profound influence. "Old perceptions" still rule, and IMO that is the biggest problem at Nintendo currently.
#4: Ow...Red headache in 3D: I think this was a mistake, but doesn't belong in the top 5. Why? Because after less than a year, nobody had even HEARD of Virtual Boy. Really. Nobody cared later. It really had a "zero" effect, as nintendo stayed on top in the "portable" market, and it wasn't meant as a replacement for a normal TV system. So while it was a massive screw-up, I don't think it affected them negatively in the market as a whole. There's other decisions (like your #5, and others not metioned) that I'd put higher than this, just because the effect was so small IMO.
#3: Mario and his hose...: I don't think this affected the company as a whole very much. Sure it was no Super Mario 64 in innovativeness, and IMO was less fun (more annoyances rather than challenges to me), but it was just an OK game, rather than revolutionary. Again, not as big a deal. I think the bigger thing that hurt the GC is that this game was NOT a release game. For virtaully every console (or perhaps 100% excluding VB), a Mario game was ALWAYS a release title. This was the bigger mistake, rather than the game itself.
#2: 2 Years after PS2: As others have said, it was less, and while I'm more in the camp of "it had a bigger effect", again, it wasn't business-shattering IMO, just from the XBOX perspective. It certainly didn't help though.
#1: Next time someone tells you CD's are the future, tell them to shut up (No CDs for N64): No shit. I think this was listed either in the top 3, or #1 in multiple "worst decisions in videogame history". If people look back at SNES, one of the main reasons Nintendo had dominance was its WIDE array of 3rd-party developers. Discarding CDs threw away Squaresoft (big mistake), but it also made an artificial "limitation" on devleopers, so that they remained "wary" of doing anything with Nintendo. The loss of developers caused by this decision was the mistake, more than the media type itself. Then they compounded the error in GameCube by not using DVDs. Their fear of piracy outweighed business sense (again) by again LIMITING what developers could do (GC discs are MUCH smaller). But snubbing Sony and not using CDs is EASILY the biggest mistake Nintendo ever made.
Now having said that, what would the video game landscape be like if Nintendo had NOT snubbed Sony, and either HAD come out with a CD-expansion for SNES (and N64 having CDs), or simply competed with Sony with BOTH having CDs? Would the rest of the mistakes put them down, or would Nintendo have stayed high?
I wonder...
