My thoughts:
Starfox 64 (Lylat Wars to me)... never owned in on the 64, and have regretted buying it on the Virtual Console, I think I was just too late to this game, and it hasn't aged well, if I could sell VC games back to Nintendo I would with this.
Starfox Adventures... I really like this game, but it is a little easy and too short, but what's there is very good.
Not played the other Starfox games.
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LoZ: OoT.... I went mental over this game the first time I played it, I generally push myself away form anything that seems to be very popular, so I never bought this for the N64, however I played it at my friends house and as I said, loved it. We took it in turns playing to complete the game over the next 3 days (only the main story, we were not great at gaming then)
I don't think of it as the best game of all time or anything, it has certainly aged a little (If I were to ignore graphical capabilities and review this game now, I would give it 85-90%... which is impressive, but not as high as it was when released)
LoZ: WW.... I still view this as my favourite game of all the ones I have played, people complained about various things in it (cell shading, triforce quest, sailing) but I loved every bit of it, and so far, although it is only last gen, I don't think it has aged at all, it's still as good as ever.
LoZ:TP.... Epicness in a box, a very fine game indeed, I do feel there was something missing to make it as brilliant as WW, and I think part of it might be originallity.
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SM64.... Again I never had this on the N64, however I do have it on the VC, and I think like OoT it has kept a lot of it's magic, perhaps more-so.
SMSunshine.... Never played it, looks fun though.
SMGalaxy.... Simply amazing, all the way from beginning to the end, after which I was very sad I had completed it and had to go back to lesser games... In my view this far exceeds SM64, again it could be my not playing SM64 in it's time, but I think I would still rate this higher even if I hadn't waited until 2007 for SM64.
Can I add a series to the mix?
Mario Kart Wii >>> Mario Kart Double Dash >>>>>>> Mario Kart 64.