You can't deny the awesomeness of the opening scene. Seeing those gloriously detailed Klingon ships cruise menacingly past the screen — and then watching V'Ger effortlessy pwn all three of them in about five minutes — must have been quite something on the big screen.
In particular the sound of the Klingons launching photon torpedoes was unusually loud and piercing.
When everyone on the bridge was freaking out because of the giant electrical tornado thing, Spock's like, "God damn it, you guys; do I have to do everything myself?" and just walks over and smashes the control panel with his bare hands, causing the tornado thing to dissipate (albeit after killing Ilia as a backup plan).
Kirk's "fly-around" tour of the upgraded Enterprise, complete with awesome Goldsmith music. Made doubly awesome by virtue of this being our first look at the Big E in 10 years, and on the big screen to boot.