Good job done with this showdown video. I think that III vs. IV was probably the best and most interesting match-up you could have gone for as I think that the two are more or less even, more so than it would have been with I vs. IV or II vs. IV.
As for III and IV I think both are a lot of fun and has a lot of good stuff; IV has the better creep factor and III has the better humor (and the 'Dial Z For Zombies' segment which is my favorite of the six; interestingly it's your least favorite) but the thing with III is that 'Clown Without Pity' and 'King Homer' isn't as strong as 'Zombies' and it's barely any creepy & IV is a little more uneven and the ending is a confused mess where they just throw everything at you. I think I'd have to pick III because it has the overall stronger jokes and that great last segment.
(And I agree that the next Treehouse showdown should be I vs. II).