When they are rescuing Spock from the volcano, McCoy's line is almost straight out of Immunity Syndrome. Enterprise in the atmosphere flying away from the volcano, reminds me of Tomorrow is Yesterday. The Enterprise being a ship out at sea, literally in the movie, was used a ruse by Kirk in Bread and Circuses. The hands on the glass a reference to Wrath of Khan. I can't wait to see the movie tomorrow. I just got the above from the trailers.
You'll probably have to see it more than once to get them all, I missed out on several important parts of the Kirk/Marcus conversation cause I was staring at the desk with all the past starships on it and then was thinking "omg section 31"