Finding Elena (BoFIV) vs Demon Path 1 (SN)- I think context hurts BoFIV here. Since context says that the villain gets away, the game barely remembers Elena outside this scene, Cray is a twat that deserves to suffer, and the only one you even feel bad for is Nina, who tries to save the scene but has a lot working against her. Soul Nomad meanwhile says "oh, so you want to be a dick this playthrough? Fine. Level 1: murder your friends and family. Dickish enough? No? You really are unbalanced, you know that?"
Forever Rachel (FFVI) vs Gorudo Battle (SuikoII)- I dunno. Both are pretty good at what they want to do. The unholy beatdown of Gorudo mid-scene though gives you that sense of just how angry Riou and Jowy were here which tips it. Which is funny since that's not necessarily how it goes outside the battle!
Lenneth v Loki (VP1) vs Now is the time! (FFX)- Oh, good, two of my noms face off. Argh. Guess I'm feeling the cheese today.
Succeeding you, Father (WC3) vs Waltz (FFVIII)- Kneejerk.
Day the Shovel Died (WA5) vs Stupid Cow (SN)- I guess I feel like the SN thing is part of a running gag that doesn't get it's best impact here.
Don Corneo (FFVII) vs Angus Redux (DMC4)- One of FFVII's oft-forgotten traits is a healthy love of subverting or inverting an uncanny number of RPG character tropes. The girls being the more threatening ones in this scene (and particularly this version of events) is one of the best examples of that, which makes it all the funnier.
Eirika and the Stone (FE8) vs DDS PLOT (DDS2)- Eirika's actions here aren't really a writing failure, for all it invokes less sympathy than it might for the sheer stupid of it. So it's hard to enjoy. TRANNY JESUS on the other hand, THAT'S entertainment.
The Black Knight vs The Killer Rabbit- I've always loved the Holy Handgrenade solution.