The main parts of your game that you should upload to the GGJ website are as follows:
The Rules (including set up)
The components (pieces, board etc)
Photos/Video of your game being played
This is the most important part of your upload, as without these no one will know how to play your game!
Your rules should be as clear and concise as possible. As you playtest you are likely to find conditions that test your rules, or bring up situations that are not covered, so try and add these in as you find them. Playtesting is an essential part of the process to try and discover any loopholes or ambiguity in your rules.
If your phases of play or turns are quite complex, try and give some example turns as part of the rule so people can follow how the flow of play is supposed to go.
Example of how a ruleset could be laid out:
About the game: Name of the game, estimated play time, number of players, credits.
Theme/Backstory: If your game takes place within a narrative, include a couple of paragraphs in italics explaining the theme and premise.
Game components: What is included in the print-and-play package, and what common components if any must be supplied by the players separately (e.g. standard dice)
Aim of the game: In a sentence or two, explain what are the players trying to do to win
Setup: What do players have to do before the game starts, to get the game ready? This includes deciding who will go first.
Progression of play: Detail what happens during the play of the game, what can players do, at what point, under what conditions, and what other things happen automatically that are not triggered by explicit player actions.
Resolution: Under what condition(s) does the game end, and when the game ends how is a winner determined.
Additional examples of turns of play or quick reference tables if required.
Don't forget to find a designer in the room to help you make your rules look good, and make them clear to follow. Add some instructional graphics to help with play, or some graphics to enhance the setting and theme.
Remember that to some extent, the game is the rules, so use the same care and craftsmanship for the rules document as you would for other components.
Further reading on this topic:
Writing Rules - from Board Game Design Lab
A thread on board game geek about Rulebook Writing
6 tips on writing rules (video) - from board game design time
In addition to the rules, you must include the components themselves, along with instructions for how to cut them out and assemble them, or files to 3D print them.
Some common components to consider including in your files:
Game board. If it is bigger than a standard piece of paper, make sure you include instructions on how to put together.
Cards. Standard card size is 3.5 x 2.5 inches. Consider making a single (separate) sheet for card backs, to allow players to print the cards double-sided if they want.
Dice. If the dice are of a standard variety (4, 6, 8, 10, 12 or 20 sided with numbers counting up from 1), just mention in the rules that the player should be prepared to supply a certain number of dice of certain types. If you want non-standard dice, include a large unfolded die for printing.
Pawns and meeple. Standard colored pawns to represent the players' pieces on the board can simply be mentioned in the rules as something the players are expected to supply themselves.
Other custom tokens.
Player aids. If your game has certain things the players need to look up frequently while learning the game consider providing a reference card to the players.
Further resources:
Ludism Wiki - Dowlondable Piecepacks, free templates for board game pieces
Putting It All Together
Ideally, you should combine everything into a single document in an accessible format such as a PDF. Or if there are other elements like 3D printed models, pop everything into a zipped folder, to upload onto the GGJ website.
It is best if you can also upload some photos and videos (you can link a youtube upload to your project) to show people playing the game, and explaining the rules. This really helps others understand your game and how it plays!