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First of all you'll need to download the Project64k emulator. It's the online version of Project 64. It can be found at the PJ64k homepage. You'll need WinZip or WinRAR to extract it, but you should already have one of the two. If not, you can find WinRAR (the better of the two) here.
Once you've done that, you'll need to open the Project64k.exe. Then we'll need to make a few adjustments:
First of all we're going to check the Plugins by going to Options > Settings...
Which will bring you to this:
If yours looks like that, then it should be fine. Those are the default plugins, don't go and start changing them (unless they absolutely don't work), because it can lead to problems when trying online. However, there is an error with the Jabo_Direct3D7 1.40 graphics plugin that leads to things such as invisible Samus blasts, flat shields, flat bombs, and some other graphical glitches. This can be fixed, though. If you try to change the plugin normally you'll get an error when trying to start up the ROM (SSB game) online, because PJ64k tries to load the plugin of the name Jabo_Direct3D7.dll. The fix is to simply take a working plugin (such as the newest Jabo plugin) and name it Jabo_Direct3D7.dll; or you can just download it here and replace the current one with it. =D This isn't necessary, of course, but I think most people would rather have no graphical glitches. Note: PJ64k tries to load all of the plugins by their default names. So if you insist on using a different plugin, change the name of the plugin you want to use to the name of the plugin already being used; otherwise it wont load correctly when trying to play online.
And finally, continuing on...
Next we'll need to set the Window Resolution so that you wont need to full screen (which you shouldn't anyway, cause then you can't talk). Sometimes full-screening can lead to desynching, which is a term you will most likely become familiar with by playing online if you aren't already familiar with it. Desynching is when both players become desynchronized during gameplay and different actions, such as your opponent attacking the air or suiciding, occur. Anyway, to set the Window Resolution simply go to Options > Configure Graphics Plugin...
I personally have mine set to 800x600. You can set it to whatever looks best for you, however I wouldn't recommend one higher than your computer's screen resolution is already set to.
Next you'll want to set your controls, that's kinda important. You can use your keyboard, which may be a bit awkward at first, but some people are pretty good players with the keyboard. I use a PS2 controller via a USB adapter (you can order USB adapters from various online stores, like Lik-Sang). To set your controls go to Options > Configure Controller Plugin...
Edit: I use an Xbox 360 controller (wired, the USB one) to play now. I recommend it if you don't mind sparing $40.00 for it. It has a nice feel to it. But if you use the 360 controller (may happen to other controllers too) the default plugin (Jabo's DirectInput 7 1.40) wont recognize some buttons, such as the L/R buttons on a 360 controller. So I had to find a different plugin that would work correctly online. Which happens to be NRage's Direct-Input8 V2 1.83. You can get it from here or here.
If you're going to used the plugin mentioned in the "Edit" section above, read the following. If not skip down to "Not using NRage's Plugin."
Using NRage's plugin:
First download the plugin above and put the .dll into your Plugins folder. Then go to Options > Settings... and select it.
Then go to Options > Configure Controller Plugin...
Make sure the Plugged box is checked on Controller 1 and NOT checked on Controllers 2-4. Also, I suggest unchecking Real N64 Range. All it seems to do for me is cause the analog stick to be less responsive when pushed in certain directions. Then set your buttons and click the "Devices" tab.
Under Device choose your controller, unless you're just using a keyboard. Here I'm using the 360 controller. Now click the "Controller Pak" tab.
Uncheck the box next to "RawData" and make sure it's set to none. This seems to only cause problems online, and as far as I know, Rumble/Mem paks aren't supported online yet. Once you've done all this, I recommend choosing "Save Profile" and saving your settings so that you can just load them later with "Load Profile" if they get messed up or something. Then click Save and exit. Your controls are now set. =D
Not using NRage's Plugin:
Under Game Device: you'll need to just leave it as None for the keyboard, or if you're using a controller set it to that. Mine is the SmartJoy Dual PLUS Adapter. Then just configure your buttons to whatever suits you. Also, make sure the "Plugged In" box is checked; which it should be by default anyway.
Aquiring the game:
For the next step you're going to need the actual Smash Brothers 64 ROM. In case you don't know what a ROM is, it's the actual game that the emulator loads and plays. ROMs are illegal, so you'll have to find a way of getting it. Either by contacting someone who has it or using a search engine (Google). Try googling: Super Smash Bros. (U) [!] or something. It's relatively easy to find.
So once you have the ROM, place it in a folder that's convenient for you. I just stick mine in the PJ64k folder. Then you'll need to go to File > Choose Rom Directory...
Then navigate to the folder that your ROM(s) are located and select it. Everytime you add a new ROM to your ROM folder you'll need to either "Refresh Rom List" or rechoose the directory. If you've done this correctly, your ROM should appear in green text in the white PJ64k box. Like so:
Assuming that you've done all of this, you are now ready to play online! So now go to File > Start Netplay...
Once you've done that a window should appear that has a list of servers. You can wait for the list to ping all of the servers and then choose one, or you can go to Enter IP... and enter the IP of a known server that you'd like to play on. Once you've entered a server you can go to the Recent tab at the top of the window instead of entering the IP or waiting for the list to refresh. Most Smashers are in the server under this IP: 69.90.34.110:27888
Make sure you keep your Connection Type at Good [20 keyframes/s], that's what most people are set to; and unless your connection is set to the same thing as the other people, you can't play with them.
But before you join any servers, you'll want to enter a user name at the bottom of the window:
My username is Myztek, so you might see me on. =b Have fun playing online! We need more good players.
Two more important things:
First of all, NEVER pick Random Stage when playing online. It will lead to desynch because the players will end up on different levels.
Second, you need to do the following to activate All Characters and the Mushroom Kingdom stage:
-First of all start up the Super Smash Brothers 64 Rom (not online) just go to File > Open Rom...
Once the Rom has loaded go to Options > GameShark Codes (Cheats)...
And you'll get the following menu, in which you merely have to check two boxes:
So from now on, when you host games you'll have all the characters.
UPDATE:
The following explains how to use "beta stages", as well as stages such as Metal Mario, Polygon Stage, etc.. Online or offline.
First of all, load up the Smash Brothers ROM. Then go to Options > Gameshark codes (Cheats)
Once you're there. Click the "New" tab, and you'll be brought to a menu to add in cheats.
Here are the codes:
800A4D09 0009 - Kirby Beta Stage 1
800A4D09 000A - Kirby Beta Stage 2
800A4D09 000B - Tutorial Stage
800A4D09 000D - Metal Mario
800A4D09 00OE - Fighting Polygon
800A4D09 00OF - Race to the Finish
Type the first part of the code in the first box, and the last 4 digits in the second box. The second box only shows a single digit, but type or paste the numbers in anyway. Then click Insert. The code should appear in the white box. Type in a description under Cheat Notes if you want to. The click Add to DB.
Now you're ready to use it. Go to Options > Gameshark codes (Cheats) > then check the box next to the stage you want. Make sure you only have one stage checked. Then load up the game, pick any stage, and you'll be on the stage of choice.
If you want to do this online, then make sure you have the stage you want checked before loading the game up online. The cheats have to be sent to the opponent when the game is started, so you can't change stages while playing. If you feel the need to change stages, you'll need to restart the emulation. Check the box of the stage you want before you close the game and restart the emulation though. Otherwise you'll have to open it seperately, choose the stage, close the game, then click "Start Game" to play online.
A note about Race to the Finish: You can't die here. The only player that can win is Player 1 by running to the end of the level. Sometimes this freezes up the game too.
* And if you don't want to manually entering all those codes yourself, you can download my .cht (cheat) file and put it in your Project64 folder, replacing the old one. You can download it here.