Well he wouldn't download them again, or he will have duplicates lol

You have a GC, so get OoT/Master Quest in the Wind Waker special edition.  If you didn't know the GC version not only comes with Master Quest (a version of OoT with remastered dungeons), but also plays in 60hz (the N64 and VC versions only play in 50hz here in PAL regions).

Super Mario 64 is amazing, but I myself prefer the DS version (puts up flame shield).  However keep in mind the VC version will be considerably cheaper though.

Super Mario Kart is a game that IMO hasn't aged too well (again puts up flame shield), that's not to say it isn't good.  I would recommend getting Mario Kart SC for the GBA as it has all the tracks from SMK.

Donkey Kong Country is another kick arse game, but I would recommend DKC2 instead as I think it is a better game.

That leaves Super Metroid and Super Mario RPG, both are amazing and I would whole heartedly recommend either of them.  Though I would like to say that if you want an RPG with Mario characters, I prefer Paper Mario to SMRPG (for the third and final time puts up flame shield).

Hope that helps!

Since Paper Mario is so much better than SMRPG I must say buy that instead but if you already have it then I must say Super Mario 64 or Zelda

If you like any of the other Mario Kart games then I recommend getting the original.  Congrats on getting 1000 points for your birthday and good luck picking a game to spend those points on :).

Man, this is a difficult choice!

Do you plan to get a 3DS at launch?

If no, get Ocarina of Time.

If you want the best single-player experience, with great exploration, great atmosphere, great music, and great storytelling, go with Super Metroid.

If you want the best tag-team co-op experience, with great music, great secrets, and great level design, go with Donkey Kong Country.

If you want the best simultaneous co-op experience, with beat-'em-up action mixed with RPG leveling, tons of secrets, and a great sense of humor, go with River City Ransom.

Whatever you do, don't download reel fishing. :D I made that mistake...

I have decided to extend the time until tomorrow. It seems that Super Metroid is dominating so far. 

I was just about to recommend that. RubangB, you are awesome!