Here are some scenarios you might wish to employ in games:

HEROES vs VILLAINS: Your team may consist of only recognizably good characters, or evil ones. Any question of the figure’s loyalty is answered by the team ability on the character base (ex. R Scarlet Witch is Brotherhood and thus a villain, E Magneto is X-Men and thus a hero, etc.). If you have a heroic team, then you can’t have any villains, and vice versa.
variations:
Marvel heroes vs. DC villains?
400 point DC heroes vs. Judge Death and Vet Fear, Fire and Mortis?

NO TEAM-UPS ALLOWED: Your team may only consist of pieces from one of the teams, or have no group affiliation. (ex. If you choose Superman ally as your team, you can pick any Superman ally characters and any unaffiliated pieces, but no others.)
variations:
JLA vs. Injustice League or Avengers vs. Masters of Evil? (note that the high cost of the IL / MOE team ability might make it more even if you give the villains an extra 25 points, or let them have one unallied villain or Minion of Doom on their team.)
X-Men vs. Brotherhood? 2000 AD vs. Titans? Hydra vs. Top Cow?

A LIMIT ON STRENGTH: The judge rolls a 12-sided die (or 2d6), rerolling if the result is a 1 or 2. The result, multiplied by ten, is the maximum number of points the strongest pieces on your force can be. That is, if the judge rolls a 10, then none of your pieces can exceed 100 points.

MAGIC AMULET: At the center of the board is a magic amulet. This amulet has a resistance of 14 to being picked up and acts as any other object on the board. It can be carried, TKed, dropped or moved by any figure; however, it has bad juju inside it, and if any character picks it up, it poisons them for one click at the start of the posessing player’s turn. On the other hand, they might want it because it increases the attack and defense of the player carrying it to 21, and whomever has it at the end of the round earns an additional 100 points.

EMPTY THE TRADE BOX (Keep What You KO): Build three separate 200 point forces using pieces you would not mind losing. When you KO an opponent’s piece, it is yours. When your opponent KOs one of your pieces, hand it over. This is even more fun if you play Round Three as a Sealed Booster event! Pull a really powerful piece you actually need and then keep it hid in the back so your opponent cannot steal it!

THE HOTDOG RUN: Your force may contain either one unique or one veteran who is the team captain and one experienced who is the assistant. All other pieces must be rookies. The team captain gains the leadership power on all clicks.
variation:
Dump the experienced assistant; just go with a Vet + Rookies.

THE DEATH OF A POPULAR DUDE: Each player must field a “villain” character with an AE base (Black Manta, Sabretooth, Magog, Mandarin, etc). This character has recently killed his arch nemesis. Every piece on the opposing team represents someone who has come forth on this day to avenge the death. The AE gains nothing additional by KOing any of his new tormentors, but anyone who knocks out the AE gets double points.

WHY A LAST MAN?: Two male characters have found themselves in the hands of angry Amazonian armies! Each player fields a team consisting of only female characters plus one male. The males’ damage is reduced to zero on all clicks. The male may be captured by rolling a successful close combat attack against his defense. If captured, he may be carried like an object, and if either team brings him back to home base without losing their own male, then they gain a 200 point bonus.

THE TRAITOR GENERAL: Place the character with the highest point cost in your army in one corner of the board and click him to his last click of health. This character cannot be healed. He has sold out your opponents. Now protect him from their mighty vengeance.
variation:
Each player places their highest point cost character together in a central location – perhaps the monitor room of the Avengers mansion map, or on a Mage Knight dungeon you’ve constructed – and each force races to get there in time!

LEGENDS OF THE SUPERHEROES (NBC, 1979): Players construct the following armies:
Superhero player: E Batman (92 pts), V Robin (22 pts), E Flash (82 pts), E Huntress (23 pts), V Hawkman (48 pts), R Black Canary (21 pts), E Unleashed Green Lantern (125 pts), U Shazam! (166 pts).
Super-villain player: Sinestro (300 pts), V Solomon Grundy (75 pts), V Weather Wizard (50 pts), E Riddler (39 pts), Mordru (109 pts).

LEGION OF SUBSITUTE HEROCLIX: Each player assembles their army in two halves: a first team and a reinforcement team. The two teams must be of equal value (within six points). When any member of the first team falls, a reinforcement arrives on the back row of your side to take their place. Reinforcements arrive in order of point cost, from weakest to strongest!

FEELING GRAVITY’S PULL: Any flying character who “taxis” another character may only move one-half their distance.

LEGION OF LOSERS (The greatest Heroclix scenario ever played!): Assemble the worst possible force you can come up with and give it to your opponent to play. Mind your opponent will do the same to you. This works best in tournament games. In each match, you will be playing against the same team – the one you assembled – while you will use a different army.
When assembling your team, pay close attention to Team Abilities and powers. Every action will count when you’re looking at big opposing forces with a maximum attack of 8. Suddenly, pieces like Blob and Toad become quite useful because they can move for free! It’s not unusual to see armies of more than 16 pieces in 400-point games. Free movement, flight and Leadership become very important. And do you really want to let your opponent use Energy Explosion against your big mass of people? variations:
Play “Shock the Turtle,” where, after round three, every piece on the map’s borders takes a click of damage. With each turn, this “energy barrier” moves closer in to the center!
Put a cap on the number of pieces – say, 300 points, no more than six pieces per team. This puts a whole new spin on it. Rather than burden your opponent with six Rookie Vampire Lackeys, you have to find higher point losers!

THE EIGHTH RANK: The objective in this game is to move your force completely across the board. Any piece which makes it all the way across to your opponent’s side leaves the game as a survivor and you take 25 bonus points. Further, when they go, they automatically KO whichever of your opponent’s pieces was closest to the space your piece entered.

COSMIC STRATEGO: This is a game for two players, each of whom fields a 500, 600 or 700 point army. One player is defending three objects, one of which is marked on the underside as being the “true” object. The other two are fakes. The defender knows which is which and may place the objects on the map however he wishes. The object can be picked up by any opponent piece which is adjacent to it. It can be carried, or thrown by any character up to four squares, or six if that character has a ranged attack.

The defender may start anywhere in the back six rows. The opponent must start in the back two under standard rules. The defender also replaces three of his Clix pieces with tokens. These represent characters whom the opponents cannot initially recognize from a distance. The tokens have a movement of 9 and no attack. They can be hit from range, (for one click of damage, if and only if the attacker rolls a critical hit). Tokens “become” actual characters when an opponent bases them, which, regardless of the opponent’s movement/speed power, ends the opponent’s movement immediately. The opponent wins the game and collects full points for his build total, plus points for each KOed defender, if he brings the “true” object back to his starting area. The defender wins if the opponent cannot do this in the time permitted, and collects points by standard Heroclix rules.

LEGION OF MONSTERS: Your teams may only consist of characters which are visibly inhuman in some way. Suggestions include Man-Bat, Solomon Grundy, Ulik, Blastaar, Beast, Fury, Ghost Rider or Hellboy.

RESCUE THE BLACK WIDOW: Nick Fury has sent Natasha behind enemy lines – again! – and the Mandarin has captured her. The “villain” player assembles a 400 point team including 200 points of “named” characters, one of whom is the Mandarin, and 200 points of generics (Hydra, AIM, ninjas) along with an imprisoned E Black Widow, who cannot act or be attacked or moved until the “hero” places one piece adjacent to her. The “hero” player assembles 360 points of superheroes. If the hero player can rescue the Black Widow, then she can assist the hero team in defeating whatever wacky scheme Mandarin’s up to this month.

THE TROIA CHALLENGE: Construct a 400 point team which includes Vet Troia. No other pieces may cost more than her 98 points. Now figure out a way to win with it.

COPS AND ROBBERS: Player one fields U Judge Anderson, E Brit-City Judge, E Judge Dredd and R Judge Hershey – 210 points and 2 actions. Player two fields any combination of Henchmen, Thugs, Lackeys and Criminals from the first two sets to make 250 points, plus the Red Skull, and gets three actions. Can the future cops take down the evil mutie gangleader Redhead and his crew?

ELEKTRA-GO-GO: WizKids has released something like fourteen different pieces named either “Elektra” or “Elektra Natchios.” Construct a 300 point team which includes seven of them.

HOSTESS CLIX: Judge creates three tokens for each map: one Fruit Pie, one Cup Cake and one Twinkie. These may be picked up by any character. They have a range of four. Any character may throw the token at any opponent character with an attack roll. If the attack is successful, the target piece gets an action token. All of its current powers on the dial, and its Team Ability, are Outwitted while the target enjoys some yummy Hostess goodness.

Judge should also bring a box of Hostess snack cakes to the game. None of that off-brand store crap either.

THE ANTI-CHEESE GAME: 600 point constructed, unrestricted. Players build their teams in secret and do not show them to anyone else. Once everyone has arrived, but before the game starts, everyone writes down their opponents' names and the name of one Heroclix piece next to it. If anyone correctly guesses that a player is using a particular piece (GRANT - JANE FOSTER or JOHN - R JEAN GREY) then the player loses that piece and plays without it. In other words, build at your peril, because if somebody figures out what you might do, you might lose a big chunk of your team. Use unpredictable pieces!