I'm looking to catch up on some of the Zelda games of the past. I've started almost every Zelda game on the native console and at some point lost interest or been distracted by another game, or in too many cases, lost the save file and never gone back to it.
With the advancements of emulation, Windwaker, Ocarina, Skyward sword and Twilight Princess have plenty of variables, some games like Ocarina can be played in a dozen different versions, on different systems, with different hacks, texture packs and so on.
So, whats the absolute best way to play these games?
For OoT and MM, the 3DS remakes, and in the case of the latter, using the patch that brings back the zora swimming mechanics, are the best way to experience those games IMO. Played in an emulator to render at a higher resolution if you like.
As for Wind Waker the Wii U version looks stunning. If you don't have a Wii U then Cemu is what you want.
Twilight Princess you could go for either the GC, Wii or Wii U versions. The graphical improvements in the Wii U version other than rendering at a higher resolution are hardly noticeable. If you go with GC/Wii they are best played in dolphin at a higher resolution, GC/Wii games don't look great on modern TVs.
Skyward Sword is best played in Dolphin, using an AR code that disables the depth of field effect, as it looks weird in HD. There's a HD texture pack for it that does a really good job at recreating the original art style. Sadly it's incomplete, but it improves on enough areas that it's worth using anyway.
Zelda BotW performs slightly better on Switch than on Wii U. The Wii U version has better lighting but the Switch version has higher render distance. You likely won't notice the difference unless you do a side by side comparison (or watch one online) though, so either is fine. If you have neither of those systems, Cemu is the way to go.
That should be all the main series games I think.
The DS entries I don't know if count as 3D Zelda games. They are technically 3D but they play more like 2D Zelda. I found them highly skippable but you may enjoy them. The best way to play them would probably be in an emulator rendering at a higher resolution (DeSmuMe supports it and I don't know about melonDS or DraStic), using the most up to date D-Pad patches so you don't have to control using the touchscreen.
Same for Tri-Force Heroes and Zelda ALBW, they play like 2D Zelda so I don't know if they count. But as opposed to the DS games, I actually enjoyed these. Especially Tri-Force Heroes, which is a blast with friends. Less of a blast with randoms where it can get frustrating trying to explain to people what to do. For these games, rendering at higher resolution doesn't matter too much I think, but you can do that if you want with Citra.