Non-Video Game examples can be found at the bottom of the page.
In Fable I, the 'evil' missions often pay better. For example, there's a quest to either attack or defend a farm, but attacking it pays 250 more gold. Also, the weapon you can get from the Religion of Evil is the best bow in the game. The weapon from the Saintly Church? Above average at best.
Fable II however is an example of the "immediate gratification vs. long-term gain" subversion. sure, you can gouge prices in the stores you own and gain property faster by massacring the townspeople (which lowers the economy and makes stuff cheaper), but high shop prices mean NPCs won't buy as much, a low economy means that you get less for selling vendor trash, and killing off a house's owner gives a permanent penalty to the value (and therefore rent). Being an evil dick will get you money fast, but being a good character will mean that you'll be making money hand over fist if you just wait and invest.
This is actually one of the major themes of Fable III -Once you become the King of Albion, you have to choose between making good and evil decisions. Evil decisions generally reward you with more money, but earn you the animosity of your people and former allies; whereas good decisions please these people but put the nation in debt, making it much harder to amass the gold you need to protect Albion.
Then again, the investment tactics from the previous game work here, and the day of invasion doesn't get any closer as long as you don't complete any main story quests. So waiting around long enough and the income from your properties can be channeled into as many beneficent programs as you like.
In the first Armored Core, similar to Fable's 'attack the farm' quest, there are two missions to either attack or defend some cargo, I believe, and attacking it pays more.
This is technically true in BioShock. Harvesting the Little Sister nets you twice as much Adam as rescuing them. In the long haul, this beats out the 200 Adam bonus for every three, but the difference is so negligible as to be pointless, and the rewards for rescuing them are worth far more than the tiny bit of Adam you get for not doing so.
In Champions: Return To Arms, the 'evil' quests tend to have a greater experience to effort ratio, and more options for massive gold farming.
A variation occurs in The Elder Scrolls IV: Oblivion, in which there's a split. The Theives'(illegal) and Fighters'(legal) Guilds would often reward you with paltry sums of gold when progressing through the ranks, but the rewards suddenly become better near the end, giving you powerful magical items and such, along with superior long-term benefits. The Mages' Guild(legal) and Dark Brotherhood(illegal) however, tend to give you the very powerful items and spells along the way, with the final rewards and long-term benefits being rather inferior compared to the former two guilds.
And that the Mages Guild if you a complete Game Breaker just for completing it halfway. And the Fighter's Guild only gives standard high-leveled loot, which you can also get by raiding a Fort or two.
In Daggerfall, your best monetary rewards actually come from a noble of slightly questionable action, Lord K'avar of Sentinel; even if you become his enemy, he will still send expensive stuff your way. The worst payments are from the noble Knights guilds, who offer you armor at different levels, and a house when you get to the top, but pay you nothing otherwise.
An uncomfortable truth in Skyrim. The Dark Brotherhood and Thieves' Guild questlines are some of the most rewarding and entertaining in the game, though the rewards of the Companions' and College's questlines aren't too shabby either. You also have to do pretty horrible things to obtain some of the Daedric Artifacts.
In just one of many examples in Knights of the Old Republic, you can give the Rakghoul serum to the bad guy (and he'll pay you), or else you can give it to the doctor, who gives you a trivial reward, but gives the cure to the people who need it. Also, many Light Side acts involve you giving piles of your hard-earned money away.
The trope alternative is true as well. The Dark Side powers tend to harm your enemies, while Light Side powers buff your existing abilities. It's a playstyle choice in a sense - Hurt your enemies or help your friends? Both yield the same results in the end.
Inverted in one instance in the second game: There's two merchants, one good, one evil. The evil one has pretty good stuff, but won't sell anything until you kill the good one. The good one will buy anything, and sell immediately, but her selection is absolute crap. However, if you decide not to kill her, getting the bad guy angry, she'll sell some of the best items near the end of the game, including some unique ones. To top it all off, when given the choice, she flat out tells you "you have two options, one that is quick and offers known rewards, the other may not pay off now, but may in the long run. Which one will you choose...Jedi?"
In fact, the Light Side / Dark Side split shows this. It's often said that the dark side offers quick, easy power, and the light side offers less power more slowly - but only the light side can give immortality, the goal of Jedi and Sith alike.
In Overlord you can spare villagers (which gives you nothing) or you can kill them (for resources). There's also a quest where you can return some food to said villagers (with the implication that they don't deserve it) or keep it (and, again, gain a massive chunk of resources).
Murdering peasants and generally cranking up your corruption rating means that the top-tier spells are more powerful than the the ones you get as a "nice" evil overlord.
Overlord II gives you the option of Domination or Destruction. The former involves subjugating peasants to make your slaves, generating resources over time. The latter is basically the Kill 'em All option, getting all of the resources at once with no opportunities to get any later.
The Demon Path in Soul Nomad & the World Eaters gives much better experience and "Gig Points." Since there's a New Game+ option, this is the best way to build your character up if you want to fight the Bonus Bosses in the main storyline.
The Baldur's Gate inverts the trope, and bigtime - sure, you get an extra hundred gold here and there, but good quest resolutions nets more XP, more unique magical artifacts, and Karma Meter bumps that decrease store prices and ultimately render your money-grubbing ways moot. The evil NPCs are individually better than their good equivalents, but since each game only has about four evil ones and good NPCs hate your guts if you do evil, your party options get severely limited. Oh yes, and you basically have to act Chaotic Stupid and embody Evil Is Petty to be evil anyhow, which makes the whole thing damn unsatisfying.
However, in Baldur's Gate 1, you're tasked with freeing a Nymph from a mage called Ragefast. You can kill him for 2000xp and loot his tower full of valuable magical artifacts and take the Nymph or let her go. Or you can say the right things to him and he'll let the Nymph go without a fight, netting you 2000xp and a lock of her hair (which you can turn into a powerful magical cloak). But if you're an asshole, you can also do both. First persuade Ragefast to let her go and get the hair. Then talk to him again and he will attack, so you can kill him. That's 4000xp, and the hair, AND the loot, without loss of reputation. This is just one example of the quests where you can do the right thing AND the wrong thing, for double the payment and no repercussions.
And then you can go back to your boss, who tries a You Have Failed Me on you. You can then kill him for another 2000xp, and loot his place for his gold and magical artifacts. Bottom line: one Nymph goes free to do whatever it is Nymphs do all day, the world is rid of two Jerk Ass wizards, and you got paid thrice. That whole storyline might as well be called "Karmic Distribution For Fun And Profit".
Similarly, a Thief in Beregost will rob you every time you talk to him, while complaining about his stolen Boots of Stealth. You can easily find his boots and give him them for gold and 500xp. Or you can keep his boots for your own thief. Or you can give them to him for the reward and then, because he's a jerk, kill him without repercussions and take them back. Who says Chronic Backstabbing Disorder isn't profitable?
It should be noted that neither of the above outcomes are treated as 'evil' by the game itself. The nymph quest does have an 'evil' outcome, which is selling the nymph to the wizard who hired you, but as we've already noted it's much less rewarding than the good or omnicidal option.
In a 'more fun' example, in Shadow the Hedgehog, filling up the dark meter gives you 'Chaos Blast', damaging everything (and charging your dark meter some more) around you, while the Light meter gives you Chaos Control, which speeds you through the level, skipping goodies and forfeiting 100% completion depending on the mission.
You're making a mistake actually using the powers in the first place. Much better is to simply hold your power, since having either gauge full gives you a both infinite ammo and invincibility. If you use it that way, there's no difference which way you're filling your gauges.
In SimCity 4: Rush Hour, taking the "bad" missions nets you a lot of money but lowers your approval rating.
SimCity as a whole tends to do this. If you're low on cash, you can bet that a sleazy character will offer you cash in order to build something for them. These tend to be things such as toxic waste facilities, missile silos, "secret" military bases, and casinos, none of which help your approval rating any.
Galactic Civilizations II gives you bonuses to your planets' development or finances should you make the "evil" choice during random events. If you choose the "evil" alignment once you've obtained researched Ethics, you'll have access to powerful ship weapons and planetary upgrades that increase loyalty to your empire, but at the cost of alienating "good" races (who will likely declare war on you shortly).
Ironically, the best bonuses for non-violent builders in the game aren't for the goody goodies, but the neutral civilizations - good races mostly get better defences, while neutrality nets you better trading ability, the best research centres, more happiness (more important than loyalty if you want tax income) and all your planets instantly terraformed. Rock on, moral grey zone.
You need avoid being a monster that no one wants to trade with you and yet not a goody two shoes that you find money as a source of evil, that is why trade is so fitting for neutral factions.
For the most part, being a goody two shoes in random events gives you penalties, while being evil gives you massive bonuses. The neutral option gives you bonuses as well, but not as much as the evil options (most of the exceptions fit this trope as well).
Averted in Metal Gear Solid 3: while you may choose to pave your way with piles of corpses, every single soldier you kill, as opposed to tranq or avoid entirely will attack you during your brief stint on the Other Side, where you face The Sorrow. If you've killed a lot, this sequence can take an agonizingly long time.. Also, defeating bosses by non-lethal means nets you their camouflage, while killing them gives you a fat lot of nothing.
Except The End, who you need to hold up to get his camo, after which you can murder the hell out of him. Tranquilizing him gets him his Mosin Nagant (if you actually went through all the trouble of knocking him out you probably will like a non-lethal sniper rifle).
Sorta inverted in Neverwinter Nights: near the end of Chapter 1 you come across a demon in a summoning circle. Choose to free him from the circle and you can get a magic weapon, a magic item, or a temporary but awesome buff. Choose to banish him and you can summon the good spirit he chased away, who rewards you with... a different magic weapon, a better magic item, or the same temporary but awesome buff. The spirit also gives you more XP, but which weapon is better depends entirely on your Character Class.
Fallout goes both ways. Evil quests pays more credits, plus the lack of moral inhibitions means you can gun down innocent merchants and take their stash if you're too poor to trade with them - but evil people generally have the best loot in the game (and unlike with merchants, there's no other way of getting said loot), and good quest solutions give more XP.
Really evil characters can become so hated that bounty hunters will attack them as random encounters on the map. At higher levels, these encounters are lethal. Unfortunately, you never become so famous that the next city has already heard of you.
In Fallout 3 being really good ALSO gets bounty hunters after you as well. Being really evil, however, can cause Raiders to become terrified of you and try to pay you off to avert your wrath.
Several quests actually lean on Evil path with better rewards: The Power of Atom quest for example: Disarming the bomb in Megaton nets you a (ramshackle, albeit noted in-game as "The Most Luxurious") house and 200-400 caps. Blowing it up, however, can net you upwards to 1000 caps and a lush, very comfortable apartment in Tenpenny Tower.
Also, in the last mission in Broken Steel add-on, you have the option to nuke two targets, the Enclave-controlled Mobile Base Crawler, or The Citadel, aka the HQ for the Brotherhood of Steel, your most loyal in-game allies. If you choose the former, your reward is...Good Feels Good and a thanks speech. Doing the latter nets you the most powerful handgun in the game (specifically, the rarest of rare version of Scoped .44 Magnum) and the satisfaction of having dealt with those Railroading idiots permanently.
New Vegas's final add on Lonesome Road repeats this, only you get the option to nuke the NCR or the Legion, the two main warring factions, or nuke neither, OR nuke both. No matter what you do you'll get a spiffy melee weapon and light armor, but for each outpost nuked it will open up a secret area with both a grenade launcher, and another very good armor. So to get maximum rewards (melee weapon, both grenade launchers, and all 3 armors) you'd need to nuke both to open up both areas. Taking the good route of stopping both launches will only net you stuff you'd get regardless.
The Honest Hearts addon actually subverts this though. At any point in the story you can opt to simply kill an important character, which immediately ends the story and gives you a quick simple fetch quest to finish off the addon, give you your exp and final weapon rewards and resumes the main game. This means you can effectively finish a several hour addon in 5 minutes. However you'll only get the full item rewards if you solve everyone's problems and finish the whole thing. The quick evil solution actually denies you rewards.
In Mega Man Legends doing bad deeds will gradually turn your character black. Doing good deeds will turn your character light blue. This trope especially comes into play when you capture the thieves who robbed a bank. If you return the money, it's a good deed and you get a small reward of 10,000$. If you keep the money, you turn dark but get 200,000$. Considering how much money it takes to upgrade some things in game, it's very tempting to be evil.
Might and Magic VII. Although the quests are essentially the same on both the light and dark sides, being evil allows you to use Dark magic which is much better than Light magic. This is because the best Light magic spells can either be used from magic pedestals which don't care which side you took, or are just a bunch of a bunch of spells you can get for the elemental magics combined into one spell. Dark magic, on the other hand, has several of the most damaging spells in the game, as well as a few unique utility spells too. Also, if you have a Sorcerer in your party, he can be promoted to a Lich which makes him immune to Body and Mind spells. The Light side has nothing equivalent to this.
So Light Magic is utterly worthless?
Not quite worthless, just less powerful and more wasted spells. Destroy Undead does Exactly What It Says on the Tin. Their best spell is still Divine Intervention, a spell that heals everything including mana but at the cost of gaining some temporary aging. Very useful for the final dungeon since you have no reason to care about eventual stats loss.
Besides, the light spells "Hour of Power" and "Day of Protection" are basically packages of every buff spell from all the other magic styles, divine or arcane (minus "Immolation" from fire magic and the all-important "Protection from Magic" from body magic), and casts these spells at four times the power of their regular variants (meaning they last pretty much all day). Add "Day of the Gods" on top of it on high level and you get a party that's basically invulnerable, and Paralysis will knock pretty much any enemy out of commission. Sure, you find pedestals that cast these spells on you — in the good faction headquarters, which is quite a ways from the last dungeons, and also rather impractical to sneak in and out of every time you want those buffs cast at you (at a considerable lower skill level than you could do yourself).
In the early phases of Total War series, it is almost needed to play an genocidal bastard if you want florins. Although further down the line it will have the off chance of generating negative vices that reduces tax income in exchange for immediate plunder. Opting for more benevolent route will give more population to rule over and thus more units and fresh bodies.
However, in Medieval II: Total War, sacking a settlement grants more money to the player than exterminating the populace outright.
Inverted in Steambot Chronicles, where taking the evil path actually causes you to miss out on a lot of neat equipment.
if aggression could be considered "evil," then Spore has a couple subversions. Befriending creatures in the creature stage usually nets you more DNA points than attacking and eating them, and befriending other tribes gets you more food than attacking them.
Otherwise, it's pretty much averted in terms of the long-term benefits of acting aggressively vs. friendly. Players actions in each stage of the game lead to specific bonuses or abilities in the subsequent stages. Some of the best are scattered across the spectrum and really only serve to compliment the play-style used to achieve them, so its hard to call any one option "better". Entering the final stage, Space, the player earns a title and a corresponding unique ability based on their overall behavior across the previous 4 stages. By far, the two most powerful abilities belong to the Scientist (who can instantly wipe out all civilization/colonization on a planet) and the Zealot (who can instantly convert an entire planet, even an alien homeworld, to join their empire). Both of these abilities are considered war crimes by NPC civilizations (right up there with the Planet Killer weapon, meaning anyone who notices will declare war against you), and both require behaving in a friendly manner in any two of the previous stages.
Played surprisingly straight for an MMORPG, Pardus' TSS (The Shadow Syndicate, AKA The Bad Guys) has jobs that pay incredibly well, and the owners of drug stations get some free resources AND better prices on the black market. The good guys, EPS (Esteemed Pilots Syndicate) gets a few bonus jobs that are otherwise perfectly normal and average, and can only buy and sell fuel on the black market.
In the Web Game The West, jobs like grave-robbing, house-robbing, coach-robbing and train-robbing pay poorly but have a huge chance of turning up some very good items that would cost you a fortune to buy - not to mention they're worth a lot too. The only offset is that you're more likely to get injured. Which isn't much of an offset since you can regain your health rapidly anyway.
Also, some of the The West quests split into being 'good' and being 'bad' (or lawful and unlawful). The 'bad' choice has a tendency to provide better rewards.
The later Civilization games do that, probably unintentionally. Razing a captured city (and slaughtering the population, destroying World Wonders etc.) is usually the easier way, since captured cities are a major pain in the backside.
Unless you keep a Great Artist at hand.
Played mostly straight with Dragon Age: Origins, where the lack of a Karma Meter means that refusing a reward will normally have no impact except the negative one in your wallet. Occasionally it may net a few approval points with your familiars, but you can just buy them some cheap gifts to make them happy instead. In fact, if you don't walk around with your "good-aligned" allies, you can freely intimidate many people into giving you greater rewards, with no adverse effects whatsoever.
In The Godfather: The Game, a lot of your income comes from shopkeepers and racket bosses you have intimidated into joining the Corleone cause, as well as Armed Blags and Bank Robberies. Trying to make money off the corpses of enemy gangsters is challenging and slow-going, with ammo costs acting as a Money Sink until you buy a safehouse with ammo for all the gun types. For a Self-Imposed Challenge you can try being Neighbourhood Friendly Gangsters and forgo any of the above, but prepare to waste a lot more time.
Occasionally, the symbiote suit in Spider-Man: Web of Shadows makes missions easier. For instance, in one mission, you can either disable a suit of armor with a Press X to Not Die sequence or just go symbiote and throw a car. This goes the other way too, as certain choices are more effective with the good choice as well.
Planescape: Torment has a variation on this in that asking for money as a reward always shifts your Karma Meter slightly towards evil. In a more direct version, Mebbeth asks you why you want to learn magic when you start your apprenticeship with her. The answer you give determines the reward you get much later in the game. One gives you a wisdom increase, one gives you an intelligence increase, and the third one gives you both increases and more experience, but also makes you slightly more evil.
Appears for the most part in Grand Theft Auto, with Grand Theft Auto: San Andreas being the one exception, sorta. Working for the nice Triad mob boss pays better than working for the heartless corrupt police officer, though you really don't have much choice in working for the evil cop since he's black mailing you into it, and as you can imagine, pays you nothing.
Also nice in GTA4 it would be more of "Evil Pays At All" with the mission where you have to choose if you kill Derrick or Francis McReary, the nice criminal brother of one of your friends or the corrupt cop (also the jackass brother of you friend). Francis pays you 20,000 dollars and you can call him three times to lose your wanted level, an ability that otherwise only your optional girlfriend has. Derrick instead gives you for saving his ass nothing.
Killing Francis does have one nice benefit- in the subsequent mission, Albanian gangsters attack Niko and Packie at the funeral, and you have to drive the hearse to the cemetery. If you kill Francis, the police won't come after you when you defend yourself against the Albanians.
The opposite occurs with the assassination of Playboy X (jerk) or Dwayne (ex-criminal who wants to get on with his life. Killing Playboy results in getting his crib as additional savehouse, with cameo clothes of GTA3's protagonist in the wardrobe. Also you become friends with Dwayne, and get a notable friendship bonus. Playboy gives you a few thousand bucks and never talks with you again.
In Tachyon: The Fringe, siding with GalSpan nets you higher-payout and easier missions and higher-tech equipment, as opposed to siding with the Bora, who can't really afford to pay you much and fly hastily-converted cargo haulers with dumbfire missiles forced to resort to guerilla tactics. It can be assumed, though, that the latter choice is the moral high ground. Indeed, the Bora ending reveals that it was GalSpan who set up Jake in the first place. This is a case of Your Terrorists Are Our Freedom Fighters.
In Chrono Cross, at one point you are asked to save Kid after she's poisoned. You can refuse; if you do this, you piss off some people, doom the Hydra and Dwarves of Home World to extinction and Razzly to being eaten by a pentapod...but you can only get Glenn, who's one of the most powerful characters in the game, if you refuse.
Early in Scarface: The World is Yours every dollar is needed. Blasting drug dealers and taking their cash would raise the difficulty level. Better to sell them the drugs and them shoot them in the foot. With a little luck, your chauffeur will finish the job. No increased difficulty level. You got the cash and the drugs back. Time to find the next dealer. Note it only works in the first level, as once Tony is known to the underworld, the hush money required to get gangs off your back will outweigh the money gained. Also, you have to use the drug trade if you want to make big bucks fast.
The franchise involves the Paragon/Renegade meters, both of them separate meters rather than the same one. Basically, making paragon choices gives you more valuable allies than resources, while making renegade choices is the other-way around. While it would be important to balance between both in most other games, here in the Mass Effect series it pays more to be either an extreme paragon or renegade, which is needed to unlock the various charm/intimidate conversation options, as well as certain side-quests. While there's certainly nothing wrong with having YOUR Commander Shepard be fully Renegade, some renegade choices might cause you to either feel bad or kick yourself later on down the road.
In Mass Effect 2 and Mass Effect 3 you have the Paragon/Renegade interrupts. Usually (with some some notable exceptions) Paragon interrupts have you doing something compassionate and caring. Renegade interrupts, on the other hand, tend to involve much cooler and spectacular options, including some hysterical Shut Up, Hannibal! moments. Even if your Commander Shepard is a total saint, some of the Renegade interrupts are way too tempting to pass up. Which only drives home how hard Dr. Archer crossed the Moral Event Horizon; there's a Paragon interrupt to Pistol Whip him in the face.
Mass Effect 2 actually has an inversion, in Zaeed's DLC loyalty mission. Taking the "evil" choice will actually reduce your pay, as the choice involves failing to do job assigned to you by your employers.
As for Mass Effect 3, it's generally averted. Paragons tend to make allies and friends with the people who they meet, while Renegades have a tendency to anger or kill them. Guess which one is more beneficial in a Gondor Calls for Aid scenario? That said, Renegade persuade options usually can gain you the same as their Paragon counterpart, and there is one notable scenario on Tuchanka where clever Renegade planning nets more overall War Assets.
In The Sims, reaching the top of the criminal career track ALWAYS pays more than reaching the top of the law enforcement career track.
In The Bard's Tale, the Evil ending in which he sides with Demon Queen Caleigh is the one that gives the Bard his happy ending. The Good ending just lands him where he started in the game: A penniless conman.
In Red Dead Redemption, with most of the Stranger missions that have a choice, the evil option is cheaper, easier, or both. Also, at very low Honor, you get the best horse in the game. It leaves if you try to get your honor back up.
But despite the Stranger missions evil options being easier, staying at low honor is actually something of a challenge as the story missions give you more honor for completing it. This can be counteracted by wearing a bandana for completing story missions, but the bandana will also stop you from getting fame as well (a number of benefits from higher fame being quite useful for a low-honor character's gameplay).
Causality-inverted in Ace Combat Zero: The Belkan War, where earning more money makes you "evil". The game's Karma Meter is based on your treatment of neutral targets and fleeing enemies: finishing them off them earns you cash and Mercenary points, while sparing them nets you almost nothing except Knight points. Mercenary path, in turn, throws tougher and more numerous bosses at you, which, again, earns you more cash than the bosses in the Knight or the middle (Soldier) path.
Warhammer 40000: Dawn of War II: Chaos Rising adds a Karma Meter (Corruption) to each of the player's squads to measure how far they've fallen to Chaos. There's only one level on the good ("Pure") side, and several more on the corrupted one. The best gear almost always adds to the squad's Corruption, the evil optional objectives tend to make the missions easier, and you get more (and better) perks by going full-on evil. On the flip side, removing Corruption requires you to either field squads with incredibly poor equipment or finish counter-intuitive bonus objectives, thus making playing the game full-on good almost meaningless. And then the squad with the most Corruption betrays you, costing you all that hard-earned gear and perks. Oh, and you also get the bad ending.
In Army Of Two: The 40th Day, the evil choices give you cash and/or weapons while the good choices tend to give you nothing. Although you do unlock a very nice machine pistol if you made only good choices before the hospital level.
This is part of Scaramanga's Not So Different speech to Bond in The Man with the Golden Gun, to illustrate the one difference between the two men as Scaramanga sees it. He can afford to live on an island paradise because he gets paid a million dollars per assassination contract, while Bond, as Scaramanga puts it, "works for peanuts; a hearty 'well done' from the Queen and a pittance of a pension".
The first version of the D20 Star Wars roleplaying game took the concept of the darkside as being a shortcut to power and ran with it literally. Using force points lets you add Xd6 to your hit rolls, allowing you to succeed at normally impossible tasks. The Light Side goes up steadily adding a single d6 per tier, but the dark side quickly jumps up to 3 and then 5, but then stops while the Light Side continues on to 6.
Evil Plan. Alice pushes aside her concerns about siding with the obviously evil Dr. Kinesis because he offers her a 300k salary per year. It isn't until she finds out that she won't be paid that she tries to quit.
In Super Stupor, Eye-Sore used to be a superhero before he got HIV from a blood transfusion. It turns out henchmen have better health insurance.