So I bought a Wii. Here's my list of games to buy:

House of the Dead 2 and 3
House of the Dead: Overkill
New Super Mario Bros.
Super Mario Galaxy 1 and 2
No More Heroes 1 and 2
Metroid Prime Trilogy
NiGHTS: Journey of Dreams
Mad World
Legend of Zelda: Twilight Princess (on Wii or Gamecube?)
Punch-Out!!
Mario Kart Wii
Sonic and SEGA All-Stars Racing
Metal Slug Anthology

These are the GameCube games I want to play:
P.N.03
Killer7
F-Zero GX
Resident Evil 0, 1, 2, 3, 4 and Code Veronica
Legend of Zelda: The Wind Waker
Ocarina of Time Master Quest
Eternal Darkness
Splinter Cell: Chaos Theory

Any other suggestions?

You know Res 2/3 & CV are just straight ports, right?

Yep, I've never played them.

I'd suggest the gamecube version of TP. Playing Zelda with waggle just felt... Odd.

Anyway, here are some other suggestions:

Gamecube:
Tales of Symphonia
Fire Emblem: Path of Radiance
Paper Mario: The Thousand Year Door
Ikaruga (if you like shmups and have neither the Dreamcast or Xbox Live Arcade version)

Wii:
Muramasa: The Demon Blade
Okami (if you never got the PS2 version.)
Fire Emblem: Radiant Dawn (highly suggested that if you play this, to play and complete path of radiance first)
Monster Hunter Tri (dunno if you mentioned this one already; throwing it in for good measure.

Opoona. Also Blast Works.

Also suggest that you check this out: http://vsrecommendedgames.wikia.com/wiki/Wii

Welcome to wii-dom!

Re: Twilight Princess... This is very interesting. The GC version was made first, but to convert to Wii, they wanted to favour right-handed people. So they flipped the entire gameworld horizontally. Link became a righty, all the maps are mirrored vs the GC version, and the sun sets in the wrong place.

There are a few other differences in controls, but to go with the 'original vision', you might wanna go GC.

I had this on the Wii, and got confused and lost re: the big picture eventually, so I quit playing. But I did enjoy a lot what I played.

Also:

For any GC games, you will absolutely want to use a real GC controller, so get one if you don't have one already.

Re: Metal Slug Anth. I have this and found the controls were too unwieldy, no matter what I tried.

Here's a review that talks about nothing but the controls and mirrors my thoughts:

http://www.gamefaqs.com/wii/932854-metal-slug-anthology/reviews/review-108621

You might be able to interpret from that how you might feel about it.

I'll throw in another vote for the GameCube version of Twilight. The Wii remote is slightly better for fishing and shooting arrows, but the game was designed for the Cube pad and by and large the controls feel much more natural that way. Plus, as Bloomer said, the world's been flipped to accommodate Link being right-handed, and it doesn't even make sense. The world map is supposed to reflect the one in Ocarina, which it doesn't on Wii.

And don't go too out of your way for a copy of Master Quest. It's just the same game with remixed dungeons, which are frankly easier than the original designs (with the exception of a few puzzles that I found stupidly difficult, such as the one in the Shadow Temple involving a Like Like). It was a great freebie back in the day but it's not worth a steep price if that's all you can find it for.

I'll add Baten Kaitos, with an asterisk. It's a card-based RPG and the story is both overblown and not very good at all. But the combat is fantastic if you're into this sort of thing.

Do you like Roguelikes? 'Cuz "Shiren."

Thanks for the tips guys.

As far as controllers go, what set-up does everyone use? It seems that to cover every possibility you need Wii Remote and Nunchuck, GameCube controller and Classic Controller (is Classic Controller Pro significantly better?). Also, does anyone have any PAL Cube controllers they don't use any more?!

Wiimote and nunchuk are essential. GC controller essential for GC games, and also covers you for 'classic' requirements in many circumstances. I haven't needed a classic controller once yet, but it may depend on your game taste.

When I bought a wii, I gave my cube and 1 of 2 gc controllers to my sister. So alas, no spare gc controller here now.

Rogue Squadron 2 on gc is sick.