Lackadaisy/WMG

Mitzi had Mordecai kill Atlas.
Oh, come on, this has pretty much been but all but confirmed. Just because a recent strip has shown that Mitzi did feel something for Atlas doesn't mean she couldn't have still had him killed.
 * Unless, of course, Mordecai killed Atlas of his own volition. Asa Sweet might have offered him a better job in return for killing his rival; the flashback scene where Mordecai gave Mitzi his gun in front of the cafe might have been him saying "I killed your husband. Consider this as my resignation." It'd be a cold, bastardly thing to do and that's right up Mordecai's alley.
 * Or or or! Atlas wasn't really a, let's say protagonist, and Mordecai had a good reason for killing him. He stayed mum about his reasons to protect the Lackadaisy and Mitzi et al, and resigned because of it.

Freckle had something to do with Rocky getting kicked out of Nina's house.
That much isn't too big of a guess, but more specifically, I think Nina specifically asked Freckle, and gave him the final call. He implied some sort of guilt as a driving force, when it came to accepting Rocky's job offer, and the fact that he saved all of Rocky's letters reinforces this.
 * I think that Rocky convinced Freckle to join him in some shenanigans and Rocky got busted by Aunt Nina because of something Freckle did (or didn't) do. Freckle didn't make the call, he just was the direct cause - which Rocky never discovered.

Either Wick, Mordecai or Viktor are going to be killed in the future.
Tracy recently confirmed on her forum that one of the main characters is going to die, so here are some possible victims (Feel free to add some more):
 * Viktor: A retired badass who has been wounded several times and has a heartwarming relationship with the local Genki Girl? He might as well have a bullseye on his back.
 * Mordecai: Yes, we know he is one of the most skillful killers in the whole comic, but that's exactly the point. No one would expect him to die.
 * He does seem to be discovering something curious, even ominous.
 * Wick: The guy is just too darn nice to live.
 * Zib: The guy is way too smooth. Plus, his dying would have a major effect on fellow characters, leading to loads of Character Development.
 * I would disagree. His dying would serve little to no plot purpose on its own. Perhaps it would be a symptom of a greater abandonment of Lackadaisy's past, but frankly, I think it's unlikely that Zib would be the victim of Tracy's pen.
 * Given his recent development and focus, including his realizing that they're circling the drain and it's a matter of going down with the ship or not... yeeeeah, I'm worried for him too.
 * Aunt Nina: Not necessarily through violence, but losing her would hit poor Freckle hard.
 * Ivy: God, I hope not, but... killing this cutie would break the hell out of Calvin, not to mention just about everyone else.
 * Rocky: You talk about somebody nobody expects to die? How about the Crazy Awesome master of the Indy Ploy? The guy we've been following from the start? The one who gets in waaaaayyyy over his head time after time, yet always seems to weasel his way out?
 * Mitzi. She seems to be slipping somewhat, mental-health-wise, and her attempts to keep the speakeasy running are starting to border on obsession. She even scares Zib with the lengths she is willing to go to just to keep a necklace her husband gave her. My bet is that she's going to die a tragic death, and that will be the end of the Lackadaisy.
 * Lacey. It's a perfect business strategy; Wick wouldn't be able to financially function without her. Killing her off would probably enable somebody to get their paws on his money without his even knowing about it, possibly bankrupting him in the process. Let's just hope that the person potentially killing her is not involved with the Lackadaisy crew.

Atlas committed suicide.
Perhaps Lackadaisy was already spiraling into decline by the time of his death. Perhaps he felt it was Better to Die Than Be Killed or arrested. Perhaps he was not as strong as the image he projected in public. Whatever the reason, Atlas May killed himself. Mordecai was the one who discovered the body and informed Mitzi; she asked him not to tell anyone so the reputation he built up wouldn't be shattered. Besides, even if the truth were told, it wouldn't fully dispel the rumors -- for who would believe such a powerful person could ever be Driven to Suicide?

the next guy Ivy dates will be named "Hobbes."

 * Don't look at me that way, you were all thinking it.
 * Nah. Her last four boyfriends have had names starting with "C".
 * Maybe his real name will begin with C, and he'll just have Hobbes as a nickname. Or vice-versa, like Calvin's nickname is Freckle.

Zib starts crossdressing when drunk.
Don't know how canon the mini comics may be, but in one he was wearing heels off-page. In another, he had lipstick smeared on his face, and when he asks, Mitzi says he put it on himself. Both comics seem to have taken place after he was intoxicated.

Zib killed Atlas.
Unlikely, considering Zib's status as the Only Sane Man and general lack of murderous tendencies. However, he doesn't seem to have liked Atlas very much judging from his conversation with Mitzi during the whole incident with the pearls. With Tracy recently confirming that Zib and Mitzi were previously in a relationship, Zib may have harbored some animosity or even jealousy depending on the circumstances surrounding the end of his relationship with Mitzi and the beginning of her relationship with Atlas.

Mitzi herself killed Atlas.
A slight variation of the first WMG. We all know that one of the strips show Mordecai with a gun in his hand, and a solemn looking Mitzi before him. He wasn't passing the gun after he killed Atlas, he was passing it before Atlas died. Mitzi was the one who did all the dirty work. Since she was his wife, she would've had ample opportunities to get close and personal with him. Maybe she had asked Mordecai for the best instrument to kill Atlas. Mordecai probably would've asked for the reason, but didn't feel the need to interfere with Mitzi's plans since she was technically his employer too.

Calvin and Mordecai will have a showdown
They're each the trump card for the Lackadaisy and Marigold gang. They're both psychotic when handling a weapon. And who would suspect a little cutie like Calvin could take down Mordecai? Eventually they will wind up fighting each other, and Calvin will probably win.
 * Tracy practically confirmed this on her Tumblr, saying "Odds that they will cross paths are very good odds."

Wick will unknowingly join Asa's crew
Wick seems to be a perfect victim for the chopping block, but what if instead of being killed, he is tricked by Asa into funding his speakeasy without knowing, such as Asa not telling him what the money is really for. Wick does seem the naive type who wouldn't suspect anything wrong.
 * His secretary Lacey, however, is not...which could put her on the chopping block as well, if she comes to know too much.

Whoever killed Atlas will be the one to die
Possibly by way of being murdered themselves. The story would go full-circle, it'd implement poetic justice, and maybe it'd end on a light note, at least.

Mordecai wasn't always a sociopath.
Various sketches of Mordecai as a child (kitten?), plus Word of God, show that he had a tenement upbringing, but showed no signs of abnormality. Something happened to him -- or more likely, to his family -- that changed him from a quiet, nerdy neat freak into the cold-hearted killer we know and love and are secretly a little afraid of.
 * Not really sure if this applies, but in the recent pages we learn that apparently Mordecai wasn't much older (if not the same age) as Ivy is now when he started working with Victor.
 * No, that totally applies. He got mixed up in the underworld at a young age (prolly to help support his family, or after he suddenly found himself without them somehow). However, there was probably a defining incident/series of incidents that pushed him over the edge. (Bobby also mentions the theory that he has a bullet fragment in his brain, which would fit.)

Serafine and Mordecai will have some UST between each other
From what I have seen so far from each other is that Mordecai can't stand working with his new partners and I have a feeling that Serafine would tease him and tell him what a killjoy he is.
 * Nothing like a little one-sided Foe Yay between colleagues, eh?

Viktor and Elsa are…close friends
Any perceived innuendo for the term “close friends” is intentional. Yes it’s implied that she’s married to Bobby, but so far it stands as just that, an implication, it’s not out right confirmed. She seems awfully interested when Ivy mentions Viktor, and both of them served in the war (him a soldier, her a nurse). Yes, I am indeed stretching thin anything even resembling logic, but that’s what WMG’s are for.
 * OP here, and Elsa and Bobby are officially married, so if there is anything going on, its not exactly kosher.

Mitzi's necklace wasn't actually made of pearls
The way Zib looks at the one he picks up may just be him reflecting on the predicament, but that expression and the description of how Mitzi got those "marbles" make one wonder...