Affably Evil: Mr. Black. Sure, he wants to resurrect the ninja mafia as a meritocratic crime syndicate, but the fact that Sam has to die to fulfill his ambitions is nothing personal — in fact, he's perfectly willing to settle for blackmailing Sam into officially denouncing his claim and then letting him go on his merry way.
Mr. Sin is usually quite open and friendly as well.
Ambition Is Evil: Mr. Black wasn't exactly a 'nice' person by any standards while a standard Blankface, but his antagonizing of Sam comes as a result of this trope: Mr. Black can't bury the remains of the Ninja Mafia until Sam is buried with them.
Ascended Extra: Future Fuzzy has so far had about ten appearances in the comics. Only four of them have been official comics and his last appearance in the strip's Canon was in 2004: He continues to have regular appearances each year in the guest comics.
Ascended Fanboy: In-universe example: Most of the Ninja Mafia's mooks and lower-level operatives appear to be ninja fanboys who signed up for the chance to be real ninjas and earn money doing it. The blankfaces are Tykebomb versions of the trope.
Big Bad: The story currently looks like it may be setting up Mr. Sin in this role. He shared the spotlight with Mr. Black for most of the Noosehead and Emperor arcs, and became the primary antagonist of "Sam and Fuzzy fix your problem". Lately, he's been locked in a villainous arms race with Hazel and Brain.
Black Eyes of Evil: Several of the Noosehead musicians, most notably lead man Sidney "The Sicko" and his second singer Nicole. Subverted as none of them are very evil at all; Sidney secretly wants to be a folk singer and Nicole is Sam's girlfriend.
Body Surf: Fridge can hop from body to body in close proximity. Well, could. Sexxica/Candice finally manages to take him out by killing every host within range, including herself.
Catch Phrase: Carlyle "I can take you where you need to go."
Cerebus Retcon: Fuzzy's Mysterious Past was initially Played for Laughs, with Fuzzy doing things like having his mother (a real brown bear, which turned out not to be his mother) visit and later claiming he sold all proof of his childhood to National Geographic for some cash and a Nice Hat. Said mysterious past, and the Laser-Guided Amnesia that erased it, are currently a major part of the comic's drama.
Cerebus Syndrome: Well, it's still mostly comedy, but now it's comedy with an overhanging plot.
Chekhov's Gun: The comic makes liberal use of both this and foreshadowing. Take theinteractions between Fuzzy and Crush in the context that Crush is Sam when compared to strips before the Ninja Emperor assassination, or this conversation between Hazel and Rexford in the context that Brain (the cat) eats people's memories.
Character Development: Sam and Fuzzy are the main examples, but also several side characters like Lance, Sidney, Gertrude... Most of the characters, come to it.
Characterization Marches On: The early comics have Sam being more socially awkward (such as having an interest in polka) while Fuzzy was a lot more sadistic (wearing a monkey corpse as a bodysuit).
The Cuckoolander Was Right: Malcom keeps ranting about crazy conspiracies, and turns out to be right about them, up to and including the space gophers. It turns out that his hairdo has been intercepting transmissions from bugs in the SinCorp headquarters.
Desperately Looking for a Purpose in Life: Sam spends much of the first arc, and arguably all of the second, doing this. His hand is eventually forced into finding one, although when it does Sam seems to find that a good thing.
Fuzzy: Sam! Where have you been? You just missed our most commercially viable adventure ever! Bullets and boobs...nonstop!
Filler Strips: Sam and Fuzzy has a set annual period for guest artists, known as the Obligatory Guest Artist Weekly Duration (or O-GAWD).
Foreshadowing: Toward the beginning of the "Noosehead" arc, Malcolm says some things that most would dismiss at first as being the ravings of a paranoid nutcase who's been breathing too many fumes, but in fact they reference key elements of the coming arc. A guest comic after the arc's completion calls attention to this.
Zig-zagged in this strip, which takes place during a flashback and foreshadows an event ten years in the future during an arc already finished. Take a bigger fall than that, indeed.
I Have Many Names: Mr. Sin has had so many names that he's actually in danger of running out of aliases.
Implacable Man: Mr. Blank. Standing in his way for whatever reason is not a good idea. In the end, it takes having his face carved up, being beat up by Sam and thrown off the side off a flying skyscraper to kill him.
In the Back: The ninja mafia usually don't fight fair. Especially not Blank, who killed Black with a sword through the back.
Killer Rabbit: The Grrbils. They intentionally cultivate this image.
Knight of Cerebus: Arguably kicked off by Fridge. Although he starts off as comic relief, his actions in the "Friday Night" arc drag Sam into the Ninja Mafia plotline that has dominated the last four years of the comic.
Mr. Blank and Mr. Black further do this after Sam gets set up as the one who murdered the Ninja Mafia leadership.
Koan: Carlyle tends to speak in koans or other forms of vague, yet always appropriate, advise.
Grrrbil leaders tend to be "the big man" in a literal sense. Taken to its logical extreme by their Don, who enforces the trope by consuming a magical mutagen that sticks him in a One-Winged Angel form.
Laser-Guided Amnesia: Someone wiped Fuzzy's memory roughly a year before he met Sam. It's eventually revealed that Hazel and Brain did it, and that Fuzzy used to be "Eric", the third member of the band.
It later turns out that Brain can do this at will and occasionally does it by accident. He's apparently wiped several dozen people all over the U.S.
Last-Second Chance: Sam, to Mr. Black. If not for Blank's interference, he would probably have taken it.
Let's You and Him Fight: How Sam keeps a couple of dangerous and moderately psychotic Ninja Mafia lieutenants busy so they don't get bored and try to off someone else. When it turns out that this is actually completely normal, Sam sent them back at it, but restricted them to nonlethal methods.
MacGuffin: In the sixth volume, "The Pit" that is guarded by the Omniscient Council of Vagueness becomes this. Hazel and Brain are after it for an unknown reason, and are systematically hunting down council members who each have "numbers", clues to its location, and stealing them. It's unknown how many numbers they've currently acquired.
Masquerade: Most of the story's weird, inhuman creatures and unsavoury criminals live in (or at least visit) the Underground, a network of hidden cavern-cities linked by tunnels stretching across the country. Normal people have never heard of it. (Although major soda companies still manage to put up billboards there. Somehow.)
Maybe the soda companies are owned by people belonging to the Underground?
Put on a Bus: Not counting guest strips, Future Fuzzy hasn't popped up since 2004, and Carlyle hasn't been seen or heard from since 2006. But the most surprising example was when Sam was put on a bus for a few months, before it was revealed that he was Hidden in Plain Sight from the beginning.
The Bus might have returned in the case of Future Fuzzy. Turns out he's a drug-induced hallucination.
Red Herring: After Sam and Fuzzy go missing after the events of the third book, the story picks up again following the roadies of Noosehead, one of whom is Fuzzy and the other two are Crush and Aaron. Both Crush and Aaron resemble Sam physically and mentally, Fuzzy has an equally familiar relationship with both, Crush shares Sam's ability to get himself into trouble, while Aaron shares Sam's at times neurotic behaviour and freaks out at the slightest mention of the Ninja Mafia. Aaron is the red herring: He's actually the ex-ninja mafioso Jackson. He even succeeds at fooling Blank, who finds out at the same time the reader does.
The entire Ninja Mafia. I mean, come on it's a Ninja Mafia. Eventually deconstructed by Sam when he (wisely) points out it's more of a cult than a mafia, run by cynical crooks who exploit what is essentially employees who are all Ascended Fanboys.
Running Gag: One notable one is "the death of 17th century chemist Robert Boyle."
Word of God is that Edwin was an unintentional reference (in fact, a recent Q&A said that a lot of his references tend to be the unintentional variety unless he specifically draws them in that way), but the timing of it still makes perfect sense.
Sid manages to make an in-universe example: When Mr. Sin attempts to pressure him into making more music for him while on the Island, Sid makes one loud, angry and vicious heavy metal song — the only one he will ever write — which is a single long tirade about what a prick Mr. Sin is and contains a Long List of things Sid wants him to shove up his- you get the point.
The Merch: Attempted subversion with the in-universe creation of Skull Panda, a character that "will appeal to alienated youths and wannabe social outcasts" by being simultaneously edgy and cute. Later played straight when the author realized the character was legitimately appealing; Skull Panda currently has two t-shirts for sale.
The Rival: Lance was this to Sam in the first arc.
Theme Naming: Early in the strip, Sam and Fuzzy adopt a cat that Fuzzy names "Butcher" (it turns out to be a lady cat). Fast forward through some half-dozen time skips and Sam has got a puppy to go with the cat, which he's named "Baker". According to Malcolm, we don't want to know about the Candlestick Maker.
There Are No Therapists: Subverted. At one point, Sam does go to see a therapist, but said therapist is both horrifically incompetent and a giant talking crab. See for yourself here.
You Can't Go Home Again: After a year of forced exile, Sam finally manages to return to the surface... only to find that nobody from his past life wants anything to do with him anymore.
Sam:(...)I think I missed it... more than it missed me.
You Kill It, You Bought It: This is how the Ninja Mafia works — at least, this is how it works if you kill the entire Ruling Council (so none of the official successors are left alive). Sam, as the only survivor of the murder of the previous Ruling Council, is therefore considered the rightful Ninja Emperor — and becomes the focus of all the plotting that comes with it. It's also the only way Sam can "step down". Since Emperors rule for life, someone has to kill him to take his place.
You Killed My Father: Fridge eventually possesses a ninja and kills DJ Positive. Candice reveals herself to be his daughter moments before she kills herself and Fridge's body at the same time.
You Will Be Spared: A somewhat dark version. When Blank kills Black, he claims to Sam that Black was his oldest and only friend, and that he made his death as quick and painless as he possibly could — but if Sam thinks he's deserved the same treatment, he is sadly mistaken.