Note: There are some years in which there are very few movies I've even seen, and more in which my pick is only slightly higher than at least one or two other films. I'm picking them at this moment based on a "what would I like to watch most often" criteria, as opposed to trying to judge absolute quality. In other words, I don't think The Princess Bride is really a better movie than Full Metal Jacket.
Second Note: Wikipedia has lists of movies by year -- I started here and worked my way forward.
1980: The Empire Strikes Back
1981: Superman II
1982: Blade Runner
1984: Ghostbusters (or Revenge of the Nerds, I can't decide!)
1985: Real Genius
1986: Ferris Bueller's Day Off
1987: The Princess Bride
1988: Die Hard
1989: How I Got Into College (Yeah, crucify me, but I loved this movie as a kid and I'd love to see how it holds up.)
1991: Terminator 2: Judgment Day (just slightly over JFK)
1992: A Few Good Men
1993: The Fugitive
1994: Pulp Fiction (One of the greatest years ever for movies -- I could pick a dozen I love almost as much.)
1995: Strange Days (Despite my love for Nixon, which is probably Oliver Stone's best movie)
1997: Chasing Amy (honorable mentions to L.A. Confidential and Face/Off)
1999: Magnolia (1998 and 1999 are both amazing years)
2001: The Lord of the Rings: Fellowship of the Ring
2003: What a terrible year! Very few movies I've seen that I really love unreservedly. I'm sticking The Rundown in here because...
2004: ...Kill Bill Volume 2 is really only included if you include Volume 1 in 2003, and I consider the two-part series to be much better than either part by itself. And 2004 also had Eternal Sunshine of the Spotless Mind, Shaun of the Dead, and Dodgeball: A True Underdog Story besides.
2005: The 40 Year Old Virgin (with Kiss Kiss Bang Bang and Sin City both getting honorable mentions
2006: Clerks II is my favorite, despite the presence of Children of Men and Borat
2007: There Will Be Blood
2008 (so far): Forgetting Sarah Marshall (Yes, better than Iron Man and Wall-E)
Obviously I've left myself a lot of wiggle room here, and there's a lot of stuff that I'd probably pick differently on another day, but it's an interesting thing to look at. Anybody want to pick a bone with anything?