I had a lot of trouble thinking of these for some reason. I guess I don't typically think of movies in terms of favorites unless they really blow me away. To try to rank them would take too much extra effort.
The Royal Tannenbaums — it's just deliciously, irresistably, unrelentingly quirky. You never know what's coming next, and the characters seem to have actual personalities, rather than just being names with well-timed lines to speak. Also, one of the plotlines is intriguing — an adopted brother and sister in love with one another.
Desert Hearts — quiet and compelling lesbian romance, likeable characterizations, very touching sex scene, and FINALLY, a movie that isn't all about men
Pitch Black — one of the best horror movies ever, I think. Maybe more like a sci-fi/horror mix (sci-fi is my favorite genre). It has a foreign feel to it that is befitting the setting (an uninhabited planet of three suns) and creates ambiance, as the viewer never gets many details about the time period, culture, origin, circumstances, etc., of the characters. Seems more realistic than most movies of the genre because the horror is supplied by very creative indigenous animals (rather than some sort of monster or masked psychopath), and because it doesn't end by having the "obvious" characters survive. I like that it does not focus on gore or drawn-out suffering.
Jurassic Park 3 — I like to see humans get their comeuppance from other animals, and I like movies that remind us to respect nature. Also, dinosaurs are just freakin' cool, and Tea Leoni is nice to look at.
(not 100% sure about this one; it might be tied for fifth place with another movie)
Equilibrium — The theme of this movie is very personal to me, as I have issues dealing with emotions and have often wished that I had less, even to the point of wanting to become a schizoid and fantasizing about having a part of my brain removed. Also, I was impressed and intrigued by Gunkata, one of the COOLEST incorporations of math into a movie I have EVER seen — a martial art based on statistical analyses of gun fights.