Boss Borot is the staple CMOF of SRW, although his subsequent appearances make him quite the Lethal Joke Character. Observe his Borot Dynamic Special, where he throws everything including the kitchen sink at his opponent.
The Xabungle characters, of course. The picture of a melon replaceing Jiron's head like in the show in Alpha Gaiden, is one of the funniest thing in the series.
Speaking of Alpha Gaiden, Roy Focker goes into one battle completely wasted. That's not the most funny part. The funny part is that this is the first time he meets Isamu Dyson, and the entire scene is fully voiced!
Also from Alpha Gaiden, when Kosuke and Uso ask Kid and Bowie how the Braiger is able to change size, they have no idea. But then their child assistants, Shin and Mei, show up and are able to explain it, though their elders still don't understand. But Kosuke and Usso do, and are even able to discuss it on a theoretical level. Cue a slight Jaw Drop from Kid and...
Bowie: Christ almighty... Kids these days are something else, huh?
Anytime Sousuke Sagara breaks out the Bonta-kun is going to be funny, with the scene from Super Robot Wars W being one long level of total awesome and laughing your ass off at the same time.
In one of the early scenarios of Z2, Celestial Being decides to stage an intervention, only to find that Dancougar Nova has gotten there and put an end to the battle before they arrived.
Lockon: Setsuna, Look at all the Gundams we got now Setsuna: ...They look like Gundams but.. Lockon: Hmm? Setsuna: I want to be Gundam like them as well Heero: Then together we shall become Gundam, Setsuna. Kira: Only through understanding can we all become Gundam Shinn: ...Will I become Gundam? Luna: Not you too...
On one stage of Alpha Gaiden, Loran and Milia bring out their mechs to do laundry since the Argamma's washing machines are broken. And then Kouji brings out the Mazinger Z to dry it with Breast Fire. One of the girls comments that he "would make a good bride," but he manages to scorch some of the laundry. Perhaps it's just as well that no one ever tries to make clothes for the Valsione or Angelg.
Incidentally, having Milia pilot an Armored Valkyrie will break the game since she has to transform from Fighter to Battloid in the cutscene.
Badass he may be in the current OG Saga, Axel Almer HAS his share of funny... when he's Ahoseru in SRW Advance. Some of his funny moments include:
When snooping on Kazuya Ryuuzaki and Erika coping to each other, he instantly blares that he and Erika makes a better couple, since they're both amnesiac, and "An amnesiac couple would be better". Cue to Kouji punching him and telling him to shut up.
When the Dragonar team was about to leave, Ken gets to have a good bye wave from his girlfriend Linda, his buddies Tapp and Light ponders on how nice it is to have a friend (read:girlfriend) wave good bye on departure... Cue to Axel waving both of them good bye, promptly disgusting both Tapp and Light, thinking that Axel is gay.
It turns out that what Lu Cain was after was in the university database, which Ryusei plays off as just minor breaking-and-entering. Once again, Rai lambasts Ryusei's foolishness, and when Sanshiro weakly agrees, the dialogue awkwardly comes out that Ryusei has implied that Rai prefers men. No excuse can save Ryusei from a severe verbal bout.
When you take down the first enemy in an Earth Route Scenario, the Skullrook uses a Spirit Command! Of course, Zuhl's "galactic" genius is not matched by his assistant, who rapidly starts pushing the wrong buttons. After a while of this (culminating in Tekagen), Zuhl furiously orders his subordinate not to use any more Spirit Commands, to Ryusei's vast amusement.
Boss is about the only one whose machine wasn't somehow handed down by the family, but Kouji observes that the Boss Borot is mainly just in the way. Boss takes umbrage at this, but with his lackeys in tow he plans to one day build the Boss Borot into one hell of a machine. Later on, Mucha shows up piloting the Borot, claiming that he's taken it without telling Boss, entitled by all the hard work he put in. He's not too worried about reprisals from Boz, who is unlikely to be able to follow all the way to space, and has even installed a Map Weapon! It also turns out that the Boss Borot's map weapon, though powerful, is totally impossible to aim.