Ok, preliminary TUC list.
The briefing was originally about a third longer.
A further scene of the Enterprise leaving dock and Kirk jabbing Valeris for questioning his orders (again.)
The klingons are given a tour of the ship, where the Enterprise's equipment for gaseous study is shown.
The dinner scene was much longer and offered more lines to Uhura, Chekov, and Scotty. It eventually broke into argument.
The trial scene was originally much longer, with whole questionings cut out. McCoy would've given a classic delivery of the line "We were framed!"
Martia mentions she was a smuggler and how her shape-shifting accomodated that.
An alternate shot of Martia's vaporization which caused controversy, as many fans saw it in the trailer and thought Kirk was to die in the film. (More on THAT in the next list.)
What's really interesting is the fact that as first filmed--it was even MORE clear Valeris didn't approve of the mission.
In the 'eavesdroping' scene she blantantly feels Kirk out about his feelings on a peace mission. After the trial she openly asks whether it's possible Kirk and McCoy DID have something to do with the assassination.
Those lines lines were wisely cut or looped.
There was also a few lines when Sulu signals Ent that he is standing by to assist Ent. First his 'com officer' (before Whitney was hired for the part)advises him that he is committing treason by offering help to Ent in conspiring to go against orders by perhaps mounting a rescue. Then after Uhura recieves his message Spock acknowledges that Sulu is putting himself in a bad position.
Once Whitney was hired as the com officer it made no sense that she'd side with starfleet against Kirk and McCoy who she had served with.
Scotty after the discussion of a BOP that can fire when cloaked says "You're talking about a dangerous new engine of destruction!" Spock replies, "yes I am.
Lines like that here and there that will never make a deleted scenes section even if we ever got one.