Darth Bastila - Bastila when she's becoming particularly grating, and when she falls to the Dark Side for real.
Jossed: Theories about the comic that have been Jossed by the creator and Lucasfilm include: Lucien Draay is Darth Sion and/or Darth Nihilus, Zayne Carrick is the Jedi Exile, and Krynda Draay is Kreia.
Missing Trailer Scene: One early trailer showed a shuttle with two Sith troopers coming out and standing guard. Then, Malak comes out of the shuttle and pull out his lightsaber.
Mythology Gag: The helmet of Kylo Ren - who is even explicitly referred to as a Knight - has a striking similarity to Darth Revan's.
They recorded the "tell me about this planet" conversations for Juhani, the same kind that you get for other party members, but they were cut from the final game. You can restore them with GameMods.
Though it is not nearly as obvious as the sequel, there is actually a fair deal of cut content. Believe it or not, an entire planet (Sleheyron) and its Star Map was cut from the game early in development. As with the sequel, there is a general restoration mod undergoing development and a Sleheyron Restoration Mod.
The Tatooine Star Map was originally housed in a Sarlacc pit.
Adding on to the Tatooine thing - there was even supposed to be an alternate plot resolution to the planet in which the sandpeople would declare you their messiah, and Czerka would be driven off the planet. Unfortunately, the necessary lines for HK-47 were never recorded, so it is impossible to restore this.
Another piece of content cut on Tatooine - it was originally possible to fight the Krayt Dragon, as the mines would only weaken it enough to be made vulnerable, but the idea was scrapped, and it is just killed by the mines.
Among the content that was still accessible through the files left in game, though, that have since been restored with mods are Deadeye Duncan from the Taris Dueling Ring appearing on Manaan asking to be able to use the name of the 'Mysterious Stranger,' the title used by Revan in the Ring, and an alternate ending for female Revan to be able to kill Bastila and remain on the Star Forge with Carth as it is destroyed.
Swoop racing was originally meant to be much more than a story element on Taris and two optional courses on Tatooine and Manaan. The only hint of what could have been was mention of swoop upgrades. Indeed there was much more planned, including customizing your own personal bike, but it was not to be.
Very early in development Bastila's role was planned to be filled by Vima Sunrider, a character from the Expanded Universe, but this had to be changed due to trademark issues. This also lead to Juhani having her name changed, as originally she was going to be named Bastila.
The game was originally planned to take place in the Clone Wars during the prequel trilogy, which could've led to the player characters interacting with people like Obi-Wan, Yoda, or Anakin. However it was decided to move the story several thousand years earlier to give the team creative freedom.
Word of God: John Jackson Miller's blog contains a lot of explanations that confirm or have Jossed fan speculation.