If you want some QoL options and modding capability then the decomp of OoT Ship of Harkinian (PC Port) will do a pretty amazing job. You have to provide your own rom of OoT in order to play it though. Though if you want to play on an emulator then what Spike and deh mentioned work fine too.
Discover Ship of Harkinian (Ocarina of Time PC Port) mods, tutorials, questions, requests, and fan discussions. Also known as SoH, this is the go-to hub for custom content and help.
Here's what I recommend for standalone emulators (if you don't want to use Retroarch):
The first two Zelda games are NES, and so either Nestopia or MESEN are your best options. For Link to the Past, you can use SNES9x, BSNES or Ares. For the GBC games (Oracle of Ages and Oracle of Seasons), I use SameBoy. For the GBA games, I would recommend either mGBA or NanoBoyAdvance. The DS games like Phantom Hourglass can be played on MelonDS.
As for the Gamecube and Wii games (like Twilight Princess and Windwaker) your only option is Dolphin. The Retroarch core I find is usually slow to update with the latest changes.
For the 2D systems (NES, SNES, Game Boy/Color/Advance) I second Ares. It's simple to use and it's nice to have a single program that can do all of them. Ares also supports N64, but it runs really hard on my computer, more so than the others. I'd recommend RMG then for N64. For GameCube/Wii, your best (only) option is Dolphin, which is really well made.
To play Ocarina of Time, I really recommend that you play 3DS version. For this, you can choose between Citra or Azahar. Citra is more popular and has more compatibility since it's older than Azahar.
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