So here's the first draft, and feel free to any more we may have overlooked and screenshots to share with everyone:
SW2: Deleted Scene Depository
After the attempted assassination on Padme in the opening, Padme and Palpatine address the senate. A particularly lengthy a moving speech opposing the Military Creation Act.
Concentrate, my Young Padawan
A short scene involving Anakin meditating outside Padme's door. You may have seen this as a Lucas Select photo.
Don't Talk Back
Anakin had more of a conflict with Obi-Wan, including a shot featuring the line, "I've heard this lesson before."
The Lost 20
Jocasta Nu (the Jedi archivist) tells Obi-Wan of the 20 Lost Jedi and about the "great" Count Dooku at length in the scene where he is looking for clues in his adventure. A bust of Dooku can be seen.
Explaining the Lost Jedi
Yoda and Mace discuss the lost Jedi who abandon the Order with Obi-Wan.
Anakin's Warning Signs
Mace converses with Obi-wan on the platform before and after Obi-1 get's in his Starfighter. Obi-Wan tells Mace of his aprehensions of Anakin taking Padme back to Naboo and he feels a disturbance in Anakin's feelings. You might have seen this shot in the SW Insider magazine.
More Remorse for Tusken Slaughter
There was more to the extended "work shop" scene with Annie and Padme after he killed the Tuskens. Anakin cries (which we saw) - but continues on where he talks of his remorse for doing it and Padme tells him that he is only human.
Padme Wants Obi-Wan
After Padme's capture on Geonosis, she pleads with Dooku to free Obi-Wan.
Up for Sentencing
In one scene filmed but forgotten, Padme and Anakin are brought before the Trial of Genoisians and sentenced to die in the Arena.
Dooku Uses 2 Sabers
Dooku fights Yoda with TWO lightsabers. Picture 1 Picture 2.
Padme's Family Scenes
Padme's family scenes were presented in some detail. All of her family was cast, but in the end they were deleted from the final cut of the film.
Padme Finishes Threepio
The still naked C-3P0 and the scene of Padme putting on his coverings. (Petersen)
Padme and Beru
Taramidala saw a promo pic at one point of Padme and Beru in the kitchen on Tatooine. I seem to remember thinking that they had a scene or two together. Unfortunately, all plot development there was cut and the Lars scene reduced to significant cameos. Picture here.
Attack of the Massifs
Obi-Wan was originally going to be attacked by Mountain beast. We saw Obi-Wan walking down a path on
Geonosis whe he was quickly drawing his lightsabre, swirling it in a fast move! He obviously killed the attacker and put the sabre back on the belt. (Hankytonk and Isopren)
Join me, Amidala
After Anakin and Amidala are captured, Dooku meets with them at the round table and tries to convince Amidala to join the separatists. (DarthZod)
Boba Will Return
Boba Fett flying away from Geonosis, no doubt his heart filled with vengeance for the Jedi, who have just killed his father. The scene I recall reading about was Boba putting on his father's helmet and jetpack and blasting from the arena. (Obiwan_1138)
Ki and Plo in Action
Filmed but not used, Ki-Adi and Plo Koon mission to blow up the Trade Federation Control Core. Thanks to Thodge for this one, and you'll remember call sheets detailing the attack and this is why when the battle ends they are to be escorted in. It is a shame, I wanted to so Plo rock the rock! The first and major scene happens during the arena battle. When Kenobi and Windu are fighting back to back Obi wan says "We need to shut down these
droid's" to which Mace replies "already taken care of". The apparently you see a group of jedi, led by Plo Kloon, fight there way into a parked battle ship and shut down the droids. The droids shut down and the jedi cheer, but then the droids power up again. (Blakeley)
Jar Jar's once had more scenes, including diplo-dialect (more mature language than Gungan) scenes. Also the laughter after he says, "Dellow Fellagates." (Hubzilla)
You Big Tease
A fantasticly written scene about Anakin teasing Padme about having Jedi powers. (bleh19)
The droid is still referenced in the film, but the SP-4 Analysis Droid (formerly PK-4) was set to appear in the film as well but was ultimately cut. (Hook)
More Jango Fighting!
Part of the Obi-wan Jango fight has been deleted. I'm not talking about the storyboards, but, when Obi-Wan comes through the doors, he ignites saber, deflects two bolts, and then the fight really jumps to him taking a swing at Jango who takes off. Now, part of the footage that was inbetween those two parts was even in the commercials and the trailer! However even if that had stayed in there was still a jump. They did film it of course, it's seen in the Fett making of documentary. (Tomcat84)
The Red Wire
Obi-Wan was supposed to be pulling the chord on the assassin droid on Coruscant which
makes it begin to fall. He tangles more wires together and it regains flight. (Rick)
Calm Him Down
Mace and Jango on both sides of the Reek trying to get to the dropped lightsaber underneath it. Mace Force-calms the Reek. (lilmacumd)
Another deleted scene was before anakin and obi wan enter the bar, they are greeted with a bouncer who says jedi are not permitted to enter. The old rumor was that Anakin ignites his lightsaber to intimidate him but Obi-Wan uses a Jedi mind trick to enter. (JZ)
Sidious to Dooku
I'm not sure if this was a scene, but you can get a lot of ideas of lost
scenes from the toys. The Count Dooku figure comes with a hologram of
Darth Sidious. So I would reason to guess that there was a planned scene
with those two in some manner. Maybe, on the Solar Sailer? (Red Two)
Obi-Wan Avoids Zam's Shots
The scene was supposed to start when Zam Fires shots at
obiwan. Obiwan senses the first shot and ignites his lightsaber with 1 hand
and deflects many bolts while holding onto the assasin droid at the same
time. As the droid get closer to Zam, the shots get harder to deflect.
Obiwan can now see the mysterious assasin a little more. One of her shots
finally hit the droid and and it hits and Kenobi goes falling towards the
lower levels of Coruscant and Zam manages to escape. (ZachMX)
Among the things I noticed missing from episode 2 was a scene that is in
the novelization, and I noticed it in some behind the scenes video.
During the chase on Coruscant, a flag obstructs one of the front engines
of the hot rod. Obi-Wan leans out over the front of the speeder to
remove it, and is almost thrown off. In the behind the scenes footage,
there's a red cloth draped over one of the engines. I don't remember
which BTS footage this was on (I've seen a ton of it over the past
couple of weeks) but if I find it again, I'll let you know. (Sio)
Boba Fett: Quick Thinker
I seem to recall a spoiler a couple of months ago about some deleted
Jango/Boba dialogue. After Boba uses the Slave 1 tail guns to run
interference and Jango manages to escape, he tells his surrogate son that he
did a "Nice job", or "Quick thinking" or something to that effect. This
didn't show up in the non-digital cut. (Damn)
R2-T7 an R2 Unit is a sneak preview figure that is to get blasted
at some point, and while a significant role may have been reduced, he can still be seen just behind Padme and her Captain Typho just prior to the Senator's ship exploding. He is blown to pieces and can be seen smodering in the debris. (Mike)
Cut Bail Organa Line
In the clone war trailer we see Bail Organa saying "we have to stop them before they are ready". Now, I have seen the film twice and did not see this in there. (Luke)
I remember a spoiler report that said Anakin force-threw a lightsaber into
an enemy (or something), like it was a spear. I think this was in the Droid
factory (or the Arena). I hope you remember hearing about this too or maybe
I am just being delusional. (Kip)
Aurra Sing Cut?
And does anybody know why George Lucas went back on his statement to
Michonne Borriague that Aurra Sing would be more prominent in Ep. II? (Chris)
Not a Little Boy
In one of the trailers, Padme calls Anakin "Ani" and he petulantly replies something like "Stop calling me that; It makes me sound like a little boy." Probably dropped because it's adequately covered in other dialogue. (David)