In the Previously On segment of the Action Comics #593 episode, a female Dr. Insano (played by Obscurus Lupa) threatens Linkara with the Tenth Doctor's sonic screwdriver. Linkara rises to the challenge by pulling out Eleven's.
A stealthy shout-out to Dr. McNinja in his ASBAR review when he sees the Irish Black Canary kicking the crap out of people. "Do the Irish have hidden ninja skills I'm not aware of?"
When a comic has someone saying "You Fool!", Linkara has taken to showing a scene from Spoony'sLet's Play of SWAT 4, right when a flash grenade thrown by his own teammate blows up in his face (followed by Spoony shouting, "GAAAAAAAAAAAH! YOU FOOL!")
"Transformers: Generation 2" title card shows Optimus Prime doing Iron Man's "Proton Cannon" super attack from Marvel vs. Capcom games.
In one episode, his way to segue into the commercial break was to dress up in a hat, carry a bow and arrow, and mutter one about wankers letting the cart move back in an Australian accent. Hiya Sniper!
The "Hell Lamp 2000" joke in his Future Shock #1 review uses the theme to Match Game as backing music.
In his "Brave and the Bold #54" review, Linkara has Batman reading about "new petitions against tax", a stock phrase in movie newspapers that was the subject of a Running Gag on Mystery Science Theater 3000.
Another example is "Our story so far: utter madness" from the Frankenstein Island Rifftrax.
In the beginning of his "Archie Giant Series Magazine #452", the song that plays, while it's "Fly Me To The Moon", it's not the Frank Sinatra version. Instead, it's Covered Up, though you still might recognize the cover from a certain show. It's interesting to note that he's singing it in the tone of the Frank Sinatra version despite the song having a completely different melody.
The final part, where he visits his son's grave, is a very well done shout out and/or homage to the first episode of Star Trek: Deep Space Nine, "Emissary".
It's likely this storyline's Arc Words ("Where do you think you are right now?") were borrowed from an episode of Scrubs which involved dealing with loss, that bad things can happen to good people, and that sometimes there's nothing you can do about it. Quite relevant to Harvey's journey here.
"I wonder what's on t.v?" *Cut's to Static* "Oh man, it's my favorite show, Candle Cove!"
And from the credits of the same episode: "My favorite episode of Candle Cove was the screaming one. What people don't realize was that it was an error at the station - The Skin taker had revealed his latest scheme and it was supposed to cut to them screaming, but the tape accidentally kept skipping back to the screaming bit. It's sad too, since the episode actually has some of Pirate Percy's best lines ever."
He refers to Ben Boxer's flying warship as a "battleplate".
Nimue sinking into madness is growing more and more familiar to SHODAN.
Among NIMUE's ramblings are references to Allen Ginsberg's Howl. note Such as "Moloch's love is oil and stone" in Brute Force #4. She can be heard faintly reciting the poem in the October 2013 trailer.