There are a lot of enemies that are based off of animals, including the Mavericks (read: Robot Masters). It can often get to riduculous levels. One of the biggest examples is the Forest Stage in X1, that had robot woodpeckers pick out robot caterpillars out of robot trees to attack our robot protagonist...
Layer is so obviously in love with Zero but the entire thing just flies over his head at Mach 1. He's so clueless it's almost adorable.
The 4Koma strips, while non-canon, are nothing but a string of hilarity. Highlights include X's Cloudcuckoolander moments and Alia being a mildly abusive Team Mom.
Other highlights include:
Axl: But the real reason I left was my copy ability. Zero:[stares] Axl: Uh, just promise me you won't ask me to change into Alia or anything...
Zero:[rapidly turns away] Like I'd do that.
It is worth noting that roughly 75% of these consist of Take Thats towards X7.
hitting bosses with certain attacks in X1-4 causes some funny things to happen.