Shout Out / Life of Wily

• To Final Fantasy IV in the February 16th comic. Proto Man is seen with Cecil's Paladin helmet, and Mega Man with Kain's. Later on, actual FFIV characters join the cast briefly.
• Mega Man tells Junk Man that if he strikes him down, he shall become more powerful than Junk Man could possibly imagine.
• Dr. Light buys a Penny Arcade shirt.
• The heroes cross the streams to destroy Grenade Man.
  Proto Man: Do...
  Mega Man: Re...
  Megatug: Megatug!
  Grenade Man: Enough with the Ghostbusters jokes, for crying out loud! Let's just Get It Over With!
• Mega Man almost says 'yippie-ki-yay, mother-' before Proto Man cuts him off.
• Cecil compares Prince Edward to 'Sir Robin without the minstrels'.
• For whatever reason, the characters sing "Wise up [It's not going to stop]" by Aimee Mann in a Filler Strip. Then, Wily starts singing "Somewhere Out There", but it cuts to Proto Man calling him a pathetic sight.
• A little later, Megatug is singing "Nobody Knows The Trouble I've Seen" by Louis Armstrong in Wily's prison.
• Mega Man and the second bird do the "Let me face the peril" conversation from Monty Python and the Holy Grail. And just like in the movie, the bird is dragging him away from a group of dangerous but attractive girls.
• Megatug does Inigo Montoya's You Killed My Father speech, despite not having a father.
  Megatug: Well, isn't that what you're supposed to say?
• The Lotus-Eater Machine they get trapped inside right after that tells them that "their princess is in another castle".
• To The Princess Bride again when the narrator is suddenly interrupted by his grandson.
• Lampshaded in self-deprecating fashion when Neon Tiger reveals he forgot about his third directive.
  Heat Man: This can't be good.
  Neon Tiger: What, ripping off RoboCop?
• The title of the July 23 2001 strip is 'Visions of Molyneux dance in his head'. Given the context, it's likely a reference to his work making god games.
• The comic gets really meta about this in the July 26th 2001 strip. Neon Tiger makes a Winnie the Pooh reference and Heat Man calls him out for being too obscure. Neon Tiger responds that just because Heat Man refused to say "By Grabthar's Hammer" in the previous strip (which he really didn't say), doesn't mean Neon Tiger has to give up on Pop Culture as well. This is immediately followed by them being sacked and the narrator announcing they've been sacked, another Monty Python reference.
• Roll is also pissed off at Wily making a Spaceballs reference, but Wily insists the strip will always be a pop culture whore.
• And yet, even he cannot actually bring himself to say "Just a flesh wound", with the title saying it instead.
• The title for the August 22nd 2001 strip is Waiting for Godot, a play known for its long, meandering and deliberately pointless conversations.
• When he cuts off Roll's hand, he tells her to stop crying or he'll also tell her he's her father.
• As the strip's reset countdown begins, Neon Tiger asks Heat Man to say something from pop culture to close out the story arc. He chooses "I would have liked to have seen Montana".
• Wily does a Last of the Mohicans reference to an unimpressed Roll.
• When the Author tells Mega Man to "do some Wizard of Oz stuff", Mega Man takes it literally and starts repeating "there's no place like home".
• Dr. Light watches MacGyver (1985) on a monitor screen, and gets mad when Neon Tiger disses it. He's quite defensive about it.
• Megatug tries using Gandalf's "Many that live deserve death" speech to justify his choice to spare Wily's life. Mega Man tells him to cut it out, and the title says he "Tolkien it One Step Too Far".
• Proto Man starts singing "Cupid" by Sam Cooke while inside Mega Man's head, believin it'll help them get out like in Innerspace.
• Shade Man greets Dr. Light and Sigma with "HOW ARE YOU GENTLEMEN?"
• Dr. Wily uses "It was you who broke my mason plate" to deactivate Mega Man. Though it's actually incorrect; it's supposed to be meissen plate.
• Sigma and Flame Mammoth have another Seinfeldian Conversation about Dark Angel and it being replaced by Firefly.
• Proto Man undergoes Sanity Slippage and starts talking like Gollum.
• The earlier Outlaw Star reference becomes a Brick Joke when Wily reactivates Mega Man with "Breakfast is signaled with a silver spoon".
• A little later, Proto Man switches to saying "All work and no play makes Proto Man a dull boy".
• And then when he finally gets the drop on Cut Man, he shoots him point-blank after saying "Dodge this".