In general, emulators are allowed, as most Pokémon runs use the in-game timer. However, runs performed on an emulator may be categorized differently than runs on console. In particular, all World Records must be performed on console to count. There are often multiple emulators for a given platform, which can vary in quality and make it difficult to find one that works well. Here is a list of recommended emulators so far know about for the various platforms.

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Gameboy / Gameboy Color

Recommended Emulator:Gambatte. Adobe pdf reader by ching liu. For the interested, the main source project is at https://github.com/sinamas/gambatte. As far as we are aware, the timing on Gambatte is exactly the same as on console.

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How do I slow down the gameboy emulator rom speed? I'm playing the pokemon blue game on the gameboy advance emulator. Initially it played at around 100% speed, but evidently I changed something accidentally that made the game speed up to about 900%, which is crazy fast and makes it just about impossible to play. My normal speed is 100%, but when I press SPACEBAR, the game lunges up to 1000% (it goes higher when I try and tinker with options), but that is insanely fast. I think the old emulator I used to use (can't remember the name) maxed the speed up feature at around 200% and that is what I am looking for.

BGB is used for Gold Glitched any% and Yellow glitched categories (NSC/151) because Gambatte does not emulate some glitches correctly. You can find it here.

VisualBoyAdvance can emulate Gameboy and Gameboy Color, but does not get timing or lag correct, so it should not be used.

Gameboy Advance

Recommended Emulator:VisualBoyAdvance-M. VBA-M is the best GBA emulator that we're aware of, but note that timings and lag may not be perfectly accurate. Windows 1703 iso.

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Nintendo DS

Recommended Emulator:DeSmuME. Expect some graphical glitches, and be aware that load times differ significantly between emulator and console, so times are incomparable. If it is running slow on your computer, try to enable 'Use dynamic recompiler' under Config > Emulation Settings (only available in 0.9.9 and above).

Nintendo 3DS

As of April 2015, there are no 3DS emulators that are able to play 3DS Pokemon games. Any emulator that claims to be able to do so right now is a scam. (This may of course change in the unknown future.)

Nintendo 64

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Project64 v1.6 is used by most runners. Runs using v2.0 are banned because of inaccurate timing shown here. Not much testing has been done on Nintendo 64 emulators' timing.