I'm pretty sure he did it at least once in the first film. "Careful with the ship, Spock. She's brand new." - Eyebrow -
All of Quinto's eyebrow raises are done by ILM in CGI. It costs 3.7 million dollars to do each time, so they keep it to a minimum...
Confirmed - just checked it. Has someone written a doctorate on Vulcan eyebrow language yet? Like left eyebrow 10 degrees means bored. right eyebrow 20 degrees amused, eyebrow in hair - you are being illogical Dr McCoy etc. Whats the effect of being mono-eyebrowed?
For some reason I excised the specific point of contention about sides... You're right. He never does raise his right brow. CURSE YOU JJ ABRAMS AND/OR ZACHARY QUINTO!!! Star Trek will forever be ruined now. The next movie should be called "Star Trek Into Eyebrows."