- most per episode in the TOS era?
- most per episode in the TNG era (incl. DS9, Voyager and Enterprise)?
- most for a TOS film?
- most for a TNG film?
- most for an Abrams-verse film?
It's going to be an effort to find all of these, so I'm just going to make this answer CW and let people fill in whatever they can find.
To start with, I found some basic information on salaries for the TNG-era cast in the TNG-era movies:
For the Star Trek reboots, Chris Pine was paid $2 million for Star Trek Into Darkness (2013), and supposedly promised $3.5 million if there was a sequel.
In addition, I know that for Star Trek: The Undiscovered Country (1991), Nimoy ensured that DeForest Kelley got a $1 million salary, since they knew it would likely be his last film job ever. However, by that point, Shatner was reportedly earning $6 million per movie.
TV Salary information is a bit harder to come by (the studios don't share as much with investors etc.), but the best information I could find claims: