Good luck with the sealed NES ones...seen those go for $1000 easily

ALttP goes for probably half that sealed

FSA came as a standalone and as a big box bundle with the GBA-GCN connector cable. Neither one was limited as far as I know...
For Minish Cap I don't think there's an all-red or all-white box, or any version other than original. The original has a white front and red sides and back. I'm about 75% sure on that...I don't have it in front of me at the moment.
Crossbow Training is a tricky one. You know it doesn't come in a regular case, right? It comes in a paper sleeve like Wii Sports for example. For this I chose to keep the whole box, zapper and all, sealed. I also have one to play with

FS AE is an eShop download only...unless I'm terribly missing something...So how could it have a player's choice version?
Here's some other titles I didn't see on your list yet:
2002 Link to the Past & Four Swords GBA
2003 Ocarina of Time & Master Quest GCN
2003 Collector's Edition GCN
2004 Classic NES Series GBA - Legend of Zelda | LoZ II: Adventure of Link
2006 Twilight Princess GCN
I know of other more obscure titles too, if you're interested, but that's all the main ones for handhelds and consoles. If you're counting digital releases too, like FS AE, then make sure you check out the Shop Channel on Wii and the eShop on 3DS for Virtual Console titles (there are several). If you're counting spin-off titles like Crossbow Training, you could include Smash Bros (all three), Soulcalibur II for GCN, and the Tingle games (all three). And just for your reference, there are several Zelda-themed hardware releases as well: Gold N64 (and controllers), various Gamecube bundles, Gold Zelda Wiimote, Gold Gameboy Camera, Gold Zelda GBA SP, Gold Zelda DS Lite (beware imitations), Silver Zelda DS Lite (UK exclusive limited to 1000, be VERY wary of imitations), and a new Black Zelda 3DS comes out on Friday!
Hope this helps dude, and good luck. As I am also pretty much doing exactly what you outlined here I'll be keeping a close eye on your progress!