GlN64 v0.4.1 - This is an open source OpenGL plugin which can be compiled on both Windows and Linux. It has relatively high compatibility with games, but its feature set is rather limited. Most people should be able to get this plugin to work on their computer.
Glide64 - This is an open source Glide plugin. A personal favourite of DeHackEd, it also has high compatibility with games and a fair amount of features, but requires Glide wrappers for people without Voodoo cards and can sometimes make bad texture decisions.
Rice 6.1.1 beta 10 - This is a cross compatible plugin that supports both OpenGL and (on Windows only) DirectX. Compatibility is high and it has a very large feature set. Also has support for High Quality texture packs made by 3rd parties. Can be quite buggy at times, so its only 3rd on the list above. Source was really opened up to the community.
Jabo's Direct3D8 1.6 - Made for Project64, but works fine in Mupen. Very good compatibility, but unfortunately works under Windows only. Has quite a few features that can be used to give games a high quality look.
Direct64 v0.5.03.25 - This is a DirectX (and as such, Windows only) plugin that has fair compatibility, but can render some complex games very well (Zelda64 and Majora's Mask, for example). Has a limited set of features, but the features it has are quite useful in increasing the quality of its output.
Rice 6.0.0 - Earlier version of Rice's plugin. Should only really be used if the above plugins have faults with your chosen game.
Jabo's Direct3D6 1.5.2 - This is an older version of Jabo's DirectX plugin which uses DirectX 6. As such, it can be used on older machines, but has compatibility problems with rendering some games. Should only really be used if the above plugins have faults with your chosen game.
Z64 - This is a highly experimental plugin in its early stages that uses low level emulation to have incredibly high game compatibility. It was created with the goal of emulating games which other plugins have severe problems. This should not be used, as the current version has many problems and may not even work on your pc, let alone others'. Listed only as it has alot of potential for the future.
TAS Input Plugin 0.6 - Input plugin made by nitsuja. It is strongly recommended that you use this plugin, as it allows for extremely high precision when TASing that no other input plugin provides.
Jabo's DirectInput7 1.6 - A good input plugin for anything that isn't TASing. Should only be used if for some reason the TAS Input Plugin fails to work correctly on a game.
N-Rage's Direct-Input8 plugins (1.60 and V2 1.80a) - These are good input plugins, but shouldn't really be used for TASing. If you decide to use version 1.6 for either playback or recording, it is vital that you go into its configuration and uncheck "Raw Data", otherwise desyncs will occur.