OK, I'll start:

BASIC TEAM-UP -- Lead character meets (sometimes unfamiliar) character under confusing circumstances; misunderstanding leads to a (usually physical) conflict; cooler heads prevail, as the two characters discover they have common goals; the two work together to deal with an outside conflict (usually, a villain or two).

Bonus points to those who can cite issue # as evidence of the plots being used. I'll crack open my Essentials some time this week.

SUPER-MINION: Behind the scenes villain grants powers to someone and sends them after the hero. This new super-minion defeats the hero initially, but is eventually thwarted, possibly leaving a clue to the identity of the behind the scenes villain.

How about "DISGRUNTLED KIN" - hero's superpowered relative, possibly heretofore unknown, turns up to cause problems.

SECRET IDENTITY: The hero's secret identity is put in jeopardy.

MATCH AND REMATCH: Hero encounters a new or upgraded villian who defeats the hero in a humiliating but non-lethal manner. Hero frets about what villian is up to and how he can possibly stop it. Villian reappears, Hero finds courage to face him and a clever trick to beat him.
(There's a variant for Team books where 'good teamwork' is the only difference between the two encounters.)

Revenge: Someone close to hero is killed or badly hurt, sending him or her on a venegeance quest.

Here are some more I can think of:

THE HUNT: The villain decides to specifically hunt down the hero. Often the villain brings in an outside expert to do so. The hero must somehow outwit and escape the villain while retaining his secret identity. Examples: Many Spider-Man stories involving Kraven, the Spider-Slayer, and evn Sabretooth (in PPTSSM under Peter David).

THE ESCAPE: The villain traps the hero, but does not kill him, usually either to gloat, savor revenge, or find out information that the hero has. The hero must escape from dire circumstances and are usually handicapped. Eventually the hero confronts the villain and escapes. Examples: Spider-Man when imprisoned by Mysterio. Any story with Arcade. The new X-Men captured by Magento in the Savage Land story by Claremont and Byrne. The DeMatteis Red Skull storyline culiminating in Captain America #300. The Lee/Kirby FF issue where Doctor Doom captures the FF and puts them in Tiny Town.

THE HEIST: Villain commits a crime. The hero tries to stop him, but fails. The hero must figure out what why he failed. Perhaps he needs a special gimmick, or to resolve a subplot bothering him, needs a MacGuffin, or merely needs to figure out where the villain will strike next. Sometimes he does not know who the villain is until later. He does and the villain is defeated. Examples: Many Ditko era Spider-Man. Early Iron Man stories with the Blizzard, Melter or Scarecrow. This is probably the most common plot, variety is only due to new villains with new gimmicks.

STOLEN WEAPON/POWERS: Villain steals hero's weapon or powers. (Green Lantern's ring, Batman's utility belt). Villain goes on rampage until hero regains weapon/powers.

alternate comedy version: comedy relief gets hero's power/weapon bumbles through an adventure until hero regains weapon/power... Examples:Pieface standing in for Hal as seen in GL Showcase; Ambush Bug and Superman switch bodies in DC Comics Presents due to Red Kryptonite exposure. (in which Ambush Bug after several calamities states that "With great power comes great responsibility... No skill, no grace, but BAGS of responsibility. ")

I quibble with the methodology so far pursued. Surely the correct approach is to choose the most archetypical stories and from them extract the archetypes. If we generate a list of archetypes without ensuring that it covers the key stories, the list won't be very useful.

In that respect, I submit the following:

"The Joker's Five-Way Revenge": Archetype: SUPER-VILLAIN SHTICK: Some super-villain exhibits their shtick until they're out-thought and out-fought by the hero. Cf. most Batman, Flash, Spider-Man stories.

"The Great Darkness Saga": Archetype: HIDDEN MASTER VILLAIN: Evil minions enact a mysterious plan until the hero figures out who the hidden master villain is and stops them. Cf. a lot of Captain America stories.

"The Dark Phoenix Saga": Archetype: BETRAYAL/DEATH OF A HERO/ALLY: One of the heroes or their allies, sidekicks, or supporting cast metaphorically abandons the hero by betraying them, dying, or both. Cf. "The Death of Superman", "The Judas Contract", "Death of Gwen Stacy".

"To Kill a Legend": Archetype: RECAP/RE-EVALUATE HERO'S HISTORY: Events cause the hero to recap his origin, learn something new therein, or re-evaluate his commitment to heroing. Cf. "Thomas Wayne--Batman", Captain America as Nomad.

"The Coming of Galactus": Archetype: PUZZLE/THREAT: The hero has to figure out what's going on and how to stop it. The focus here can be the former, intellectual, or the latter, melodramatic/horrific. Cf. most Adam Strange stories (and indeed most of Julius Schwartz's Silver Age dominion), Mr. Mxyzptlk stories, Marvel monster stories.

Don't ever forget that Silver Age staple, "Hero pretends to be evil, tries to kill his girlfriend/his sidekick/destroy the world, for various convoluted reasons usually related to duping the villain."

I'm seeing some variations on a theme here instead of truly different plots. Some of these should be rolled into one plot category and the plot perhaps renamed to better reflect it.

Super-Minion, Match & Rematch, and my own Heist is basically the exact same plot with some variances. You could add another category called the Chase and it's all still the same.

I think "Revenge" is more a stock motivation, rather than an actual plot. I also think most of Greg's suggestions would fit into one of the larger plot categories, although his contributions does fit the usual variations of the plots.

Stolen Weapon & Powers is one of the 6 plots though. However, we would need to expand it to cover any difficulties associated with the power. Spider-Man feeling sick and thus cannot defeat Doctor Octopus is one example. A new form of Kryptonite. A head injury that deprives Daredevil of his radar sense. A nega-bomb that deprives the FF of its powers. Odin deprives Don Blake of turning into Thor. Captain America is being killed by own super-soldier serum.

The hero pretending to be evil is close, but likewise needs to be expanded. This is basically whenever the hero must disobey authority. It's Thor being judged by Odin for bringing Jane Foster to Asgard, Steve Rogers turning in his identity and shield rather than work directly for the government, Spider-Man being pursued by cops because he was framed, Diablo corrupting the Thing's loyalty, or any manner of villain brainwashing a hero. Reasons may be noble or ignoble. In error by the hero or by the authorities. A misunderstanding or temporary lapse of reason. In any case, the hero is thought to have done a crime.

Here may be the 6 plots:

Basic Team-Up
Hunt
Escape
The Crime (Heist/Chase/Minion/Schtick/Master Villain/Rematch)
Difficulty with Powers
Hero turns to Crime

I think the vaguely generic "The Crime" has many variations, and is the most popular plot by far.

The reason for many variations is what "complication" is added to the plot. If we can generally agree on the six plots, we could run down what are the most typical complications.

A simple definition of plot is A, then B, hence C.

A is the status quo.
B is the thing that changes the status quo
C is what happens because of B.

The plot hinges on what B is.

Is it the arrival of a new hero or ally? Is it being captured? Is it being pursued and having to protect yourself? Is it a problem with your powers? Or that you must defy legitimate authority? Or is it the commitment of a crime?

Where things get interesting are in the complications, and the combination of plots into a single story.

The Dark Phoenix Saga is not a plot about Phoenix leaving the team. The STORY is her death, but the plots are:

a) Team up with Kitty Pryde
b) Being hunted by the Hellfire Club
c) Being captured by Mastermind
d) Having difficulties with the power of Phoenix
e) Phoenix turning to crime
f) The fight to save Jean Grey from the Imperial Guard

The story actually hits all 6 plots which is why it's has depth.

I would not be surprised if after reviewing other classic and beloved storylines, we see that they too incorporate many plots in the course of the story.

My favorite Avengers story was the 4th Masters of Evil by Roger Stern. That has:

a) Several Avengers stop the Crimes that involve the Masters recruting new members (Moonstone and Yellowjacket)
b) The capture of the Avengers and their failure to escape.
c) Captain Marvel's difficulty with powers because Blackout neutralizes them
d) The hunt of the hospitalized Hercules
e) The team up with Dr Druid
f) The successful resolution of the escape.

We don't have all six plots here, but we do have several of them. Furthermore, we have additional complications because plots b & f are technically the same, but is interrupted by the other plots.

This may be under the "crime plot" umbrella, but I think the "all my foes against me" formula is a common one. The villains decide to join forces against a foe where they had individually failed. Often they are foiled by internal squabbles, lack of trust, co-operation, etc. (sometimes manipulated by the hero himself). I'm thinking of the Sinister Six, Dr.Doom and Namor's first team-up, and of course Dr. Nobody's assembling Green Goblin, Electro and Vulture in the classic cartoon (where they're defeated by Spidey's ventriloquism!).

Also I think one of the basic six plots must involve secret identity being somehow in jeopardy or otherwise complicating matters (maybe in conjunction with the "frame-up", as in, "I know that's not the real Batman because I'M THE REAL BATMAN, but how do I explain..?").

Hmm, I don't know that we can generalize to plots in superhero comics because, frankly, most of these guys don't really care about plots. Superhero comics do have a sort of shorthand they use, however, which allows them to introduce certain concepts and ideas to their readers without the readers deciding that the writer must, in fact, be on drugs.

That said, here are my candidates for if not plots, then conceits:

1) Inappropriate social commentary. (GL/GA in the 1970's.)

2) Everything changes (Batman moves to a penthouse, Peter Parker becomes a substitute teacher, Dr. Strange becomes a dark sorceror)

3) Fill-in writer who has apparently never read the book before takes over for an issue (Marty Pasko on Impulse)

4)The Alternate realities Universe story. (Earth-1/Earth-2 crossovers)

5)Superhero must do his job while being distracted by other concerns.

6) Whole issue fight scene

I would posit a plot of "indirect threat," where the villain tries to get around the hero's puissance by threatening innocents-- planting 6 bombs around the city for the Flash to disarm, or kidnapping Aunt May, and so forth. It calls for the hero to solve the problem in different ways from the "fight" plot, and means different things about their heroism and their relationship to others.