Had I known about this beforehand, I would have done it for the prior seasons (I still might). Without further ado...
Good Times with Weapons vs. Quest for Ratings:
Good Times with Weapons is the episode where Butters gets a ninja star in his eye while they play with weapons they bought at a trade show. It is best remembered for its mocking of the Janet Jackson Super Bowl controversy and for the stylized animation for several parts of the boys fights.
Quest for Ratings is the episode where the boys are doing a news show and face constant cancellation for not getting good ratings, especially compared to Craig's 'Animal Close-Up with A Wide-Angle Lens.' They win, but discover the cost of a successful show.
Who Should Win: Good Times with Weapons for the biting commentary. I could have done without the Butters in the dog pound section, but otherwise, it manages to mock the 'controversy' at the time while still telling a funny and engaging story. Quest for Ratings is entertaining at stages, but is definitely one of the lesser episodes from the season, and the ending felt arbitrary.
Stupid Spoiled Whore Video Playset vs. You Got F'd in the A:
Stupid Spoiled Whore Video Playset is the Paris Hilton episode.
You Got F'd in the A is the You Got Served episode.
Who Should Win: Stupid Spoiled Whore Video Playset (by a hair). Paris Hilton is an easy target, but the episode is more mocking those who emulate her. It has a rather hilarious speech from Mr. Slave on how it isn't great to be a whore, plus it references The Death Camp of Tolerance (which is a better episode than both of these). You Got F'd in the A is a nice piss-take on You Got Served, and the Butters finale is hilarious, but the episode is fairly forgettable outside of the ending. The real tragedy is that one of these episodes is going to make the second round when they are easily the two of the weaker entries in an otherwise strong season.
Cartman's Incredible Gift vs. Up the Down Steroid:
Cartman's Incredible Gift is the episode where Cartman pretends to be psychic and keeps accusing the wrong people for a series of murders while Kyle tries to get the police to go after the real culprit.
Up the Down Steroid is the episode where Cartman tries to get into the Special Olympics by pretending to be retarded (thinking it will be an easy win) while Jimmy starts taking steroids for the same.
Who Should Win: In a nail-biter, Up the Down Steroid. Both of the main plots are funny and engaging (I particularly like the speech Kyle gives to Cartman about how he will go to Hell if he gets into the Special Olympics) with slightly more memorable moments than Cartman's Incredible Gift. But this was a tough one to call (both are better than the last matchup - see the travesty of the seeding?)
AWESOM-O vs. Something Wall-Mart This Way Comes:
AWESOM-O is the episode where Cartman pretends to be a robot to get dirt on Butters, only the discover that Butters has an embarrassing tape of him.
Somethign Wall-Mart This Way Comes is the episode where Wal-Mart starts killing all the businesses in town, so the boys try to find a way to destroy it.
Who Should Win: Something Wall-Mart This Way Comes. AWESOM-O is amongst my personal favorite episodes, but the satire on Wal-Mart in the other episode plays to all the strengths of South Park as a show: Biting social commentary surrounded by incredibly crude humor. But I would be okay with either winning. And you see how awful it is that one of these two will be out while Stupid Spoiled Whore or You Got F'd goes on?
Goobacks vs. Douche and Turd:
Goobacks is the episode where people from the future go back in time to get jobs, so that the money can be saved up and go to their future families. Because they work for so cheap, the people of South Park lose their jobs, and the men decide to 'go gay' to prevent the future from happening.
Douche and Turd is the episode where, because of PETA protests, South Park Elementary must choose a new mascot and it comes down to either a Douche or a Turd. Since Stan refuses to vote, he gets exiled from the city.
Who Should Win: Douche and Turd, easily. Goobacks is not without its charms ("This is way gayer than the man pile!"), but Douche and Turd cranks up the ridiculousness to insane levels and pulls humor from every single scene while mocking every character Stan interacts with.
Woodland Critter Christmas vs. The Passion of the Jew:
Woodland Critter Christmas is the episode told in rhyme where Stan helps some woodland critters prepare for Christmas, only to discover that he is inadvertently bringing about the birth of the Antichrist.
The Passion of the Jew is the episode about The Passion of the Christ. Cartman starts turning confused townspeople into Nazis, Kyle wants to apologize for the Jews killing Jesus, and Stan and Kenny just want their money back.
Who Should Win: Woodland Critter Christmas. The Passion of the Jew is more likely to win (just for the Cartman stuff alone), but Woodland Critter Christmas comes from out of left field and slowly builds into a giant, wonderful clusterfuck of inappropriateness at its climax. It literally has everything. So vote for it!
The Jeffersons vs. Pre-School:
The Jeffersons is the episode where Michael
Pre-School is the episode where a former schoolmate who was wrongly sent to juvenile detention instead of the boys gets out and tries to get his revenge on them. The boys try desperately to avoid just desserts.
Who Should Win: Pre-School. Both of these episodes are more story-driven than most (except for some light satire on Michael Jackson fans w/r/t the police framing him), but to me, Pre-School has the stronger laughs. Seeing various characters in the hospital for Indian sunburns, charlie horses, and other childhood pranks is a nice surreal touch, as is people's clueless reactions to Miss Claridge's various states of distress.
There are my votes. Feel free to tell me yours in the comments (and make sure to go vote at the website linked at the top of the page).