I do have to say this:
When I made my previous post, I was hell-bent on making either SMB3 or SMW as my Favorite Game of All Time, along with their respective system as my Favorite Game System, mainly because they were widely regarded as the best Mario games ever made.
BUT, a few days ago, I decided to make the N64 my Favorite Game System. NOT because of what other people think of it, but because of my own personal experience with the system.
Long story short, I love everything about the N64: Its design, its accessories, and more importantly, its game library. It may not have had as many games as the NES and SNES (or even the GC), but the brilliant quality of the games it does have more than makes up for it! My first system was a SNES, and I played my fair share of it as well as the NES when I was a kid, but as soon as the N64 came out and I got it for X-Mas that same year, it pretty much dominated the rest of my childhood!
Now, I was gonna make Super Mario 64 my Favorite Game of All Time to go with the N64, but it hasn't been holding up very well as my favorite, and like you said, probably because I'm forcing it to be. However, even though it's been a long time, I've been falling in love with Mario Party 3 all over again, and even though it'd seem like too much of an obvious choice, I really do like playing Ocarina of Time (even though (sad to say) I've never beaten a Zelda game before in my life. It'd be one helluva goal to work towards though, and I'm up for it...) Also, Super Smash Bros. comes the closest to what I envision every time I think of a dream game (A DC Comics VS Marvel Comics fighting game using the SSB engine).
So in short, it's now between Mario Party 3, Ocarina of Time, and Super Smash Bros. I would say at this point, "What do you guys think?", but then again, it's not about what you guys think, it's about what I enjoy the most. So I'll get back with you on this...
EDIT:
Instead of just flat-out jumping to another game as my Favorite Game of All Time (like I usually do and which never ends well), I instead decided to re-evaluate Super Mario 64 as my Favorite, and determine why it deserves to be my Favorite, and not just because it's for the N64...
Super Mario 64 has given me MANY magical feelings, like you said a Favorite Game of All Time should accomplish. When I first got my N64, my first two games for it were the two launch titles, SM64 and Pilotwings 64. I played SM64 a LOT more than Pilotwings, even though I really enjoyed that game as well. However, I loved SM64 so much and was so excited about it, that whenever I was asked to do the family prayer at the dinner table, I would throw in "Please help me to get all the Stars in Super Mario 64!" until my dad threatened to take away the N64 if I didn't stop doing that :P . Also, I've said before that if I could pick any one place where I'd feel absolutely at peace and good about everything, I would go to The Secret Aquarium (from SM64 obviously).
Obviously I've been playing SM64 just as long as I've been playing the N64, and it's had just as much of an impact on my gaming life (and my life in general) as the N64 has. So yes, Super Mario 64 DOES deserve to be my Favorite Game of All Time, and I'm proud to call it that.