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.
Speaking of the refitted Enterprise, it shows just how much more powerful the ship has become that when she is subject to the attack mentioned above that wiped out Klingon cruisers with ease, the Enterprise tanks it with no damage and only moderate strain on the shields. Even if she couldn't have kept that up for a second attack, it was ridiculously awesome.
V'ger itself. Say what you want about it, but that thing is beautiful.