Let's see what we can come up with.
Northern Division
#1 Lord of the Rings: Fellowship of the Ring (2001) vs #16
Shrek (2001) Very tough, but go with LotR
#8 Monty Python & the Holy Grail (1975) vs #9
Twelve Monkeys (1995) -- argh! Forcing me to choose! **sigh** Holy Grail it is, then
#5
The Matrix (1999) vs #12 Pirates of the Caribbean (2003) -- that's easy. One I will watch again, the other I wouldn't

#4 City of Lost Children (1995) vs #13
Pete's Dragon (1977) -- see above
#6 Ghostbusters (1984) vs #11
Carrie (1976) -- and the flowers are still standing!
#3 Indiana Jones & the Raiders of the Lost Ark (1981) vs #14
Hellboy (2004) -- while I really like Hellboy, Raiders is just a better film

#7 Galaxy Quest (1999) vs #10
Time Bandits (1981) -- tough choice again; in the end Galaxy Quest. It was a helluva thing
#2
Close Encounters of the Third Kind (1977) vs #15 Shaun of the Dead (2004) -- Shaun. Easy.
Eastern Division
#1 Alien (1979) vs #16
Fallen (1998) -- Alien, I suppose
#8
Crouching Tiger, Hidden Dragon (2000) vs #9 The Haunting (1963) -- The Haunting. Better ghosts

#5 Spiderman (2002) vs #12
Metropolis (1927) -- While I like Metropolis, it does feel a bit dated. I go with Spidey.
#4
Robocop (1987) vs #13 Rocky Horror Picture Show (1975) -- Gimme Riff Raff in this pair-up

#6
Plan 9 from Outer Space (1959) vs #11 The Fifth Element (1997) -- Plan 9 is amazing in it's badness. Fifth Element was fun

#3 Sleeping Beauty (1959) vs #11
Creature from the Black Lagoon (1954) -- glack. If I actuall have to choose one, I'll go with Disney
#7 20,000 Leagues under the Sea (1954) vs #10
Dragonslayer (1981) -- hold my nose and go with the Nautilus
#2 Aliens (1986) vs #15
Dark City (1998) -- Aliens. Game over, man.
Southern Division
#1 Brazil (1985) vs #16
Cube (1997) -- This is a contest?? It's all about Scapirelli hats!
#8 Star Wars Episode IV (1977) vs #9
The Exorcist (1973) -- Hmmm, interesting pair. I'll go Star Wars (NOT "Episode IV" -- I prefer it's true name, rather than later additions.)
#5 Princess Bride (1987) vs #12
Big Trouble in Little China (1986) -- Princess Bride. Hands down and easy.
#4 Bram Stoker's Dracula (1992) vs #13
Akira (1987) -- I have to choose one of these? Ych. Ummm.... Okay. Dracula, I suppose...
#6 Hellraiser (1987) vs #11
Total Recall (1990) -- Another one? If forced to watch one, Hellraiser.
#3
The Mummy (1999) vs #14 The Adventures of Robin Hood (1938) -- The Mummy is nice, but Errol Flynn is classic

#7
Planet of the Apes (1968) vs #10 Minority Report (2002) -- Well, I suppose Minority Report. Slightly more watchable.
#2 Dr. Strangelove (1964) vs #15
High Plains Drifter (1973) -- Both brilliant, but in utterly different ways. In the end, I have to go with the superior quality film. YEEEha!
Western Division
#1 Bladerunner (1982) vs #16
The Scarlet Pimpernel (1934) -- **sigh** I'll go with the potential of Bladerunner, rather than how it has worked out...
#8
Willy Wonka and the Chocolate Factory (1971) vs #9 Batman (1989) -- Joker trumps Oompa-Loompas
#5 The Thing (1982) vs #12
Sleepy Hollow (1999) -- oh yuck again. Ummm, if forced, I'll choose The Thing, but neither one of them for me, quite honestly.
#4
King Kong (1933) vs #13 The Seventh Seal (1957) -- Monkey okay, if viewed in right light. Seveth Seal is a classic and brilliant.
#6
Camelot (1967) vs #11 Nosferatu (1922) -- No challange. Nosferatu.
#3 Star Wars V: The Empire Strikes Back (1980) vs #14
Conan the Barbarian (1982) -- This is a challenge? Empire all the way!
#7 Frankenstein (1931) vs #10
Phantom of the Opera (1924) -- Ooooh! Tough choice! I think I give a marginal tip to Frank.
#2 Three Musketeers (1973) vs #15
Spirited Away (2001) -- not even close. Gimme D'Artangan every time!