Crowning Moment of Funny: Godzilla bodyslamming Megaguirus. The icing on the cake is that there's an upclose of shot of Megagurius looking up with the closest thing to an Oh, Crap! the prop can get before Godzilla falls down on it.
Designated Villain: Godzilla isn't nearly as destructive in this film as he usually is. He goes on maybe one or two rampages through the city and the only reason he does is because of the reactor which the characters note is like a freaking beacon to him. This makes the lengths the protagonists go to in order to kill him border on extreme at best (they make a satellite that shoots black holes and tears holes in the fabric of space and time).
Nightmare Fuel: The scene in which the two teenagers are attacked, killed, and eaten whole by the Meganulon is easily one of the creepiest scenes in the whole series. Especially since it's one of the few times in the entire franchise we see a monster actually eat people.
This, however, is not visible in the Japanese cut. The American version had the contrast of the film changed, which made the wires visible.
The battle between Godzilla and Megaguirus is a mess of sluggish editing marred by frame rate errors and speed alteration artifacts (or "ghosting"). This is especially notable, as most consumer grade editing software allows the editor to disable such resampling.