THIS POST GOT WAY RAMBLY, SO HERE'S A TL;DR / CONDENSED VERSION:
I have and have played all versions, most recently the VC, and have found it to look and play awesomely on the merits of it not just rendering at 480p but also that it runs more smoothly than both previous versions (making easier things like quick-spins and twirling into all the hoppy plants as a Deku scrub before they disappear).
However, the lack of a rumble feature combined with the fact that Majora's Mask has the Stone of Agony effect as a default attribute that Link has from the get-go... saddens me a little. That's the only complaint I would make that I wouldn't also make of the Gamecube version (which actually just refers to me preferring to use the N64 controller, for mainly Hero's Bow aiming / ocarina playing reasons... and also for small/careful movement reasons).
Cheers! Now here's the original post for anyone who's bored enough to read it:
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I've had & played all three main versions, N64, GCN CE disc, and as of earlier this week the VC version.
I've been enjoying the VC version very much so far.
I noticed the game looked crisper, and figured that it was (and it pretty obviously is, looking closely) indeed being rendered at 480p; I was initially trying to remember - recalling the fact that the game requires the expansion pak to run - whether the original N64 version ran in 320x240 or the doubled 640x480 which one or two of the expansion-pak oriented N64 games employed (such as Star Wars: Rogue Squadron); looked it up, and as I'd thought the answer is indeed 320x240 like most N64 games.
Then I remembered essentially, "Wait, I've the Gamecube version too... did IT look this good too? I mean the Gamecube also outputs and 480i/p... And I do seem to possibly recall it looking better as well..." so I went to look up whether the GCN version also did that (as opposed to just the original 240i output stretched across your TV, or some form of upscaling I suppose), again to find that it indeed does
render at double N64 resolution too.
I think the reason I had that bit of mental confusion is a cross between A) I hadn't played [any version of] Majora's Mask in a long time, and more importantly
as has been said in this thread already, the VC version
runs better.
I still get minor sound glitches from pausing the game and things of that nature, though they might be more transient than their counterparts in the Collector's Edition version - I can't recall.
But besides that minor sound issue, which really doesn't bother me, the game does seem to run at a smooth, steady pace, whereas the previous versions slow down based on how much stuff is going on. A good example of this for me is the patch of bushes in North Clock Town (it's one of the Kitsune mask bushes):
I often spend much of my first 3-day cycle as a Deku scrub twirling through as many can of these hoppy bushes (then leaving / coming right back to rinse and repeat) to grind money - ideally 9 rupees as a time (as I believe that's the total number that always comes out if you successfully destroy all the bushes before they hop out of existence).
I have gotten pretty good at twirling, TWIRLING TOWARDS FREEDOM! *ahem* good at twirling all the bushes away in a beautiful twirly bush busting dance, but on the N64 and GCN versions am not always successful in getting them all. In the VC version, so far, I've found that I'm almost always successful in getting them all and without much trouble. This has got to be due to the game not slowing down and wavering in speed once I start to twirl into the bushes. On my good bush-twirl runs on the VC console version so far, I've found myself having twirled 'em all ahead of time, and I can't precisely quantify it, but I mean ahead of time by a significant enough amount that I'd react to it like, "Wow, I don't think I ever got them that fast in the other versions!"
Anyway, one thing that does upset me a bit is the lack of a rumble feature, combined with the fact that Majora's Mask has a built-in Stone of Agony effect... which of course is useless without the rumble feature. =( So yeah, same exact singular true flaw as OoT's VC version, I suppose. Besides the fact that it's impossible to plug an N64 controller in and use that instead (well actually I believe it is if you buy a cheap 3rd party adapter.. something I'm gonna be looking into actually), as I don't particularly enjoy using the GCN controller for either Zelda 64 game.. for a few main reasons: 1) The GCN control stick is springier and responds far too sensitively for my tastes in the Zelda 64 games, especially where it comes to looking around / aiming your bow (but also to things like carefully walking forward just ONE little step, etc). 2) No C buttons. =( Completely different, and awkward button layout with no button alternative available for C-up. This mainly annoys me when it comes to a very trivial but enjoyable part of the way I play OoT and Majora's Mask: playing the ocarina as in like, really playing it, like it's a real musical instrument, which it kind of is I suppose. I'm sorry to brag or what-have-you, but with an N64 controller, I can use the ocarina to do things like playing along with the entire melody of Epona's Song / Lon-Lon Ranch theme while hanging out over there. I really should record a vid of me doing that some time and put it on YouTube.. people might enjoy that...
Oh my GODS do I ramble. For the benefit of humankind, I'll stick a TL;DR version at the top now before posting this (and leave the TL;DR intact for any of the somewhat rare type that does enjoy reading a long ramble here and there). Cheers!