Ambiguously Bi: Yoko has a lot of female friends, with whom she shares a very close bond (especially Khany and Ingrid). But she also is in some sort of relationship with Vic (see Dry Docked Ship) and has shown attraction to a male Vinean once revealed to be an android.
Angst? What Angst?: Played with Mieke. At first, she freaks out when she travels from 16th century to modern time. Later in the series, she travels to Vinea and ancient China and she has adapted quite nicely.
Anticlimax Boss: Gobol. He's Vinean genius in robotics and has a whole space city of Mecha-Mooks doing his bidding. He doesn't age thanks to the emissions of vinadium and can spam energy beams from his hands. Lyco simply blows up his energy diffuser, causing him to age rapidly and turn to dust.
Broken Base: Time Travel first being invented in 1934 as opposed to 39th century as established in an earlier story. Some fans had a hard time believing it could be achieved with pre-WWII technology while others fans pointed out this was possible in other sci-fi works such as H.G Wells' The Time Machine.
Creator's Pet: Emilia seem to be taking that route, having co-star with Yoko three stories in a row. Leloup imagined her as a lead character for a new series set in the '30. Realizing he couldn't commit to two series at the same time, Leloup introduced her in Yoko's universe.
Dry Docked Ship: Yoko and Vic/Ben. A rare in-canon example where the writer himself has chosen not to pursue Yoko's relationship because he felt it would upset the many fans who were "in love" with Yoko themselves. In a similar vein, none of Yoko's many friendships (almost exclusively with women) are given sexual overtones, in spite of the platonic love between characters.
Ensemble Dark Horse: The Vineans. To think they were initially meant to be one shot characters.
Professor Zimmer. Since that he mentioned working on Wotan's fire in the 30', he could be a former Nazi scientist.
Hegora is the tyrannical queen of the abyssal city. Should anything happen to her, the city will cease to function and die. After Hegora is disposed, Yoko is made the queen so the city could endure. However, unlike Hegora, Yoko is not an android and doesn't have backup bodies. What will happen when Yoko pass away?
Improbable Age: Word of God is that Yoko is "fresh out of adolescence", which would make her in her early twenties. Yet she is a skilled engineer and jet pilot, speaks at least 4 or 5 languages, and is a martial arts expert, among other things.
Les Yay: Yoko tends to pick up a lot of female friends, and tends to become very close with them.
Khany's Secret contains the most undertones of this, especially after The Reveal that there is an artificial human-vinean hybrid to which Khany gave cloned organs of her, and some brainwaves from Yoko, making her their spiritual daughter. Then there is the unfortunate wording of a commentary from the author explaining he did not show Khany and Yoko making up after being somewhat at odds during the story, because "they were going to reconcile in private, away from everyone."
Lost Aesop: In the The "Celestial Barge", Yoko's friends wonder why she doesn't take Morning Dew with them in their time travel. Yoko replies that she's doesn't want to risk losing her in the past. Except, Yoko forgot she already brought her time-traveling with her in two other stories, not to mention twice in another galaxy.
Magnificent Bastard: Mac Nab has some shades of this towards the end of "The Prey And The Shadow".
Nightmare Fuel: At one point, the villain of the day pins Yoko's neck to a support beam with a screw clap.
Strangled by the Red String: Pol and Mieke. There's little interaction between the two and yet, they both fall in love at the end of their adventure.
The Scrappy: Emilia MacKinley. Leloup said that fans wanted to strangled the life out of her the moment they laid eyes on her. This was due to a bad first impression Emilia made when she nearly rammed Yoko and refused to apologize. She mellowed her jerkassiness later on, but the damage had been done. Some fans say she's not that bad and is similar to other obnoxious girls likes Myrka or Litsy. As stories goes on, regulars (like Vic, Pol, Morning Dew and Mieke) having less appearances and Emilia taking a larger role, there's no end to the debate.
Values Dissonance: Yoko's grandfather buying a Chinese servant in Hong Kong for her mother. Back in the late 19th century / early 20th century, this was generally accepted, but it is unthinkable today.
Villain Decay: Ito Kazuky is much less of a villain in "The Rhine Gold".
Win Back the Crowd: In "Khany's Secret", Khany has a more active role after being relegated to a minor character in her last appearances. She's even on the cover along with Yoko. On the other hand, Emilia's role has been reduced.