Megatron coughing during his maniacal laughter was not scripted - his voice actor David Kaye really coughed during the recording session, and the animators decided to leave that in as a gag.
The Tyrannosaurus head that Megatron has for his right hand seems to have a consciousness of its own, as we can see it move its eyes when Megatron is asleep. He later brushes its teeth, and even pats his hand "on the head", but it is never clear whether the hand can act independently from its master. Most likely, these are just visual gags.
The way the Maximals defeat the Predacons without resorting to their weapons echoes the slapstick comedy gags seen in old Looney Tunes cartoon shorts. Inferno, for example, falls to the ground Wile E. Coyote-style.
Megatron is talking to himself with Waspinator in the room and mentions how the upcoming power concerning the alien disk will be "beyond imagination". The tag line for the original 1986 Transformers the movie was "beyond good. Beyond evil. Beyond your wildest imagination. " Then the Vok take on the form of Unicron's head in the very next episode.