My best setup/settings for 'GoldenEye 007' (N64) Nintendo 64 emulation on the PC.

What you will need;
1. Project64 v1.6
2. Jabo's Project64 v1.6.1 update patch (includes Jabo's Direct3D8 v1.6.1 (latest version at this time))
3. Project64 Unofficial RDB v4.22 by Nekokabu & MASA
4. Azimer's HLE Audio v0.56 WIP2 (latest version at this time)
5. Hacktarux/Azimer HLE RSP v0.2 from Mupen64 v0.5.1 (only the 2005 90KB recommended)
6. N-Rage Input Plugin V2 v2.2 Final (latest version at this time)

Firstly you need to get Project64 v1.6 and then apply Jabo's Project64 v1.6.1 update patch.
Once you have done this go to where you installed Project64 and replace the 'Project64.rdb' file with the unofficial RDB v4.22 by Nekokabu & MASA. This will automatically give you most of the current/best settings for game accuracy and performance.
Now you need to add three plugins to the plugins folder. Azimer's HLE Audio v0.56 WIP2 and N-Rage Input Plugin V2 v2.2 Final are available individually. For Hacktarux/Azimer HLE RSP v0.2 plugin (only the 2005 90KB release recommended) you will need to get it from the Mupen64 v0.5.1 emulator release. You will need to rename the original Project64 'RSP.dll' to 'RSP.backup' and then rename 'mupen64_rsp_hle.dll' to 'RSP.dll' thus switching the RSP plugin's over.

Now to setup everything in Project64 v1.6.1;
1. Press [Alt] [F] for 'File' menu and click 'Choose Rom directory...' to select where your game roms are stored then press [OK] button.
2. Press [Alt] [S] for 'System' menu and make sure 'Limit FPS' is ticked.
3. Press [Ctrl] [T] for 'Option/Settings' window. Go to the 'Plugins' tab and make sure these are listed;
a) Video (graphics) plugin = Jabo's Direct3D8 v1.6.1
b) Audio (sound) plugin = Azimer's HLE Audio v0.56 WIP2
c) Input (controller) plugin =  N-Rage Input Plugin V2 v2.2
4. Press the [OK] button.
5. Press [Alt] [O] for 'Options' menu and click 'Configure Graphics Plugin'. Untick the 'Hide Advanced Settings' box and press the [OK] button.

To setup everything in Video Plugin;
1. Now get back to the 'Configure Graphics Plugin' window and some new tabs should be available. Set everything up as follows;
Under the 'Settings' tab:
a) 'Window Resolution' = Whatever you want, I just choose 640x480 which is usually a 2x aspect ratio zoom for the N64 display.
b) 'Full Screen Resolution' = Whatever you want, at a bare minimum I choose 1024x768 32bit or similar for a less pixelated display.
c) 'Tripple buffer Vsync' = I set this option to remove the unwanted horizontal screen tearing that you would otherwise notice.
d) 'Ansiotropic Filtering' = I set this to atleast 8x which is sufficient to clean up any depth pixelation, producing a very crisp/clear picture.
e) 'Full-Scene Antialiasing' = A trade off between jagged edges and picture smoothing/blurring. Usually 4x for smaller resolutions and 2x for larger resolutions. Try 2x to begin with and see what you think.
f) 'Super2xSaI textures' = Doubles the native size of original textures which can make them appear sharper.
g) 'Always use texture filter' = I do not use this. Manual says cause's more problems than it fixes and should only be used if specifically told to.
Under the 'Advanced' tab:
a) 'Adjust game aspect ratio to match yours' = I do not use this. Probably help with widescreen displays although will stretch either horizontal or vertical.
b) 'Use legacy pixel pipeline' = This can help with modern graphic cards. I noticed much nicer looking textures with this turned on.
c) 'Force alpha blending' = I do not use this. Manual says cause's more problems than it fixes and should only be used if specifically told to.
d) 'Wireframe rendering' = I do not use this. With this setting everything will be shown only as wireframe's so only good for debugging,etc.
e) 'Use Direct3D transformation pipeline' = Depends on your video card. If you notice a strange looking border at edge of screen try turning this on. Worked for me.
f) 'Force Z compare' = I do not use this. If you notice objects showing up in front of others you could try turning this on. Only if needed and I didn't need this.
g) 'Copy framebuffer to RDRAM' = I do not use this. Supposedly used to disable the 'jumbotron' board in Mario Kart 64 for performance issues.
Under the 'Rom Settings' tab:
a) 'Emulated Width' = native resolution width of N64 game. Normally just leave default which is 320, this is the standard width for NTSC and PAL N64 games.
b) 'Emulated Height' = native resolution height of N64 game. Normally just leave default which is 240, this is the standard height for NTSC and PAL N64 games.
c) 'Direct3D Clear Mode' = I leave as default which is none. Can cause problems and should only be used if needed. Try it if you have black screen problems or screen clearing problems.
2. Press the [OK] button when done.

To setup everything in Audio Plugin;
1. Press [Alt] [O] for 'Options' menu and click 'Configure Audio Plugin' and set as follows;
a) 'Dynamic Audio Sync' = I leave as default which is ticked. Fixes pops and crackles if the game or emulator was to run faster than the audio.
b) 'Emulate/Simulate AI' = I leave as default which is ticked. Does an amazing job with the already turned on 'Limit FPS' option in Project64.
a) 'Force Old Audio Sync' = I do not use this. Project64 is excellent so does not require this, may cause problems with games so don't touch.
2. Press the [OK] button when done.

To setup everything in Controller Plugin;
1. Press [Alt] [O] for 'Options' menu and click 'Configure Controller Plugin'. Set your keys/buttons as you like with the following notes;
Under the 'Controls' tab:
a) 'Plugged' = Whether N64 emulator will see the device or not. You obviously want this ticked.
b) 'Analog Stick Range' = I set 50% as I find a good balance of 'sensitivity' and 'usuable range' of my logitech gamepad analog stick controls.
c) 'Analog Stick Real N64 Range' = If on then the range has a circle pattern like with real N64 controllers. If off then the range has a square pattern like PC controllers which I prefer.
Under the 'Devices' tab:
a) 'GamePad Deadzone' = I set 5% as I like a little 'give' before player movement and also eliminates any chance of controller 'jittering'.
Under the 'Controller Pak' tab:
a) 'RawData' = Turns controller pak support on. From the pull-down menu I choose 'Rumble Pak' for Force-Feedback with my gamepad.
b) 'Force-Feedback Device' = Choose your Force-Feedback gamepad from the list.
c) 'Constant Force' or 'Ramp Force' = I choose 'Ramp Force' as it felt more responsive with my gamepad.
d) 'Visual Rumble' = I do not use this. Suppose to make screen blink when Force-Feedback would happen but created a blinking title bar so don't use.
e) 'Rumble Strength' = I set 75% as a good starting point. Up to personal preference if you want a stronger or weaker Force-Feedback effect.
f) 'Test Rumble' = Press this button for a good way to quickly test what your Force-Feedback settings feel like.

Now the important setup of the games RSP settings;
1. First you will have to 'right-click' with your mouse on the game in the Project64 browser window and select 'Edit Game Settings'.
These should already be set by the Project64 Unofficial RDB v4.22 by Nekokabu & MASA but you can check with the following;
CPU core style = Recompiler
Self-modifing code Method = Change Memory & Cache
Memory size = 4 MB
Advanced Block Linking = Off
Default Save type = Use First Used Save Type
Counter Factor = 1
Large Compile Buffer = Ticked
Register Caching = Ticked
SP Hack = Ticked
Use TLB = Ticked
Delay SI Interupt = Unticked
RSP Audio Signal = Unticked

NOTE:
These settings may require a powerful computer, so try disabling some of these if you have issues:
Larger 'Full Screen Resolutions'
'Double buffer Vsync' or 'Triple buffer Vsync'
'Ansiotropic Filtering'
'Full-Scene Antialiasing'
'Super2xSaI textures'