A guide to setting up EPSXE's plugins can be found here: http://forums.ngemu.com/showthread.php?t=85600 just remember that pcsxr uses the same plugins and the info can be used for setting up that one too.
Don't use simulated BIOS, download and use a real BIOS. Any BIOS file in that package will work.
- 3D: PEOPS OpenGL 1.78 - Comes with PCSX-R. Has an anti-jitter function labeled "GTE accuracy", rendering at native screen resolution, Bilinear texture filtering and allows driver-forced AA . Despite being open source this plugin wasn't updated for years either(except FPSE version) and cant use shaders like Pete's OpenGL2 and gpuBladeSoft. There is also optimized, modified and enhanced versions of this plugin in active development which can currently be used only by FPSE.
- Pete's OpenGL2 2.9 - More accurate and compatible than OpenGL 1.78. It allows you to set a custom rendering resolution of up to 3x horizontal internal resolution and up to 4x vertical internal resolution for within the fullscreen box, aka window resolution and has support for shaders and Bilinear texture filtering. Unfortunately this plugin is closed source and wasn't updated for years.
- PeteOpenGL2Tweak-PeteOpenGL2Tweak is a PSEMU Pro compatible plug-in that patches PeteOpenGL2 plugin on runtime and adds GTE Accuracy hack.
- 2D: Edgbla's gpuBladeSoft 1.42a - Very accurate and has support for up to 6x internal resolution , Improved Coordinate Accuracy, shaders/filters and Bilinear texture filtering but renders everything on CPU, is single-threaded and poorly optimized so can be very demanding at high resolutions. Fairly buggy past native rendering resolution as well, with texture misalignment issues and whatnot. Similar Pete's OpenGL2, it is closed source and has not been updated in years, but there is some hope author will release new version
- GSDX: GSDX development is primarily focused on PCSX2 but can also be used in PSX mode. Its limited to software rendering and can increase internal resolution up to 4x but has inferior feature set compared to PCSX2 mode still its notable for being one of few open source PSX plugins which can increase internal resolution. So there is hope for improvement if PCSX2 developers ever decide to emulate PSX in PCSX2.
- Modified PEOp.S. Soft GPU Plugin with Zenju's xBRZ filter.
- New PSX GPU Plugin AmiDog its again closed source.
- Asmodean's PSXFX shader pack 1.30 Final has more antialiasing shaders than 1.5b 
- P.E.Op.S 1.10b - Recommended for most games and setups (in order to use turbo, the mode needs to be set to 2: Async Simple; it will not work with 3 or 4).
- Eternal SPU 1.50b2 - Useful for the few games/PCs that have issues with P.EOp.S.
- spuPeopsSound (XAudio2 fix for PEC) v1.10
- P.E.Op.S. DSound Audio SPU Version 1.9
- LilyPad latest SVN (The plugin comes with PCSX2, go into the plugin folder and pull out the file that says lilypad.dll and put it in the plugin folder of the emulator you plan on using). Set keyboard input to raw also, otherwise you wont be able to use hotkeys.
- Pokopom Xinput Pad Plugin
- ePSXe Shark Enhanced (adds additional features to ePSXe, e.g. pad plugin support)
- Nuvee (provides mouse and lightgun support in PCSXR)
- padGnneco (old plugin providing NeGcon support in PCSXR)
Use the following if you're using a PS3 controller:
- LilyPad-SCP (Comes with the SCP driver, which is a very nice alternative to MotioninJoy)
- LilyPad-MotioninJoy (if you've a DS3 and are using MiJ)
This pack has preconfigured versions of both the regular and SCP versions of lilypad:
- PSX Emulation Cheater(PEC)
These PS1 emulators do not use plugins, in case you want something that just works and is more accurate.