Evil Is Bigger

The David Versus Goliath plot is where the hero is the underdog in comparison to the villain. One of the easiest ways to have this come across visually to audiences is to literally make the villain physically larger.

Aside from the villainous characters themselves being big, their tools and resources also tend to be bigger. If the hero has Powered Armor, the villain has a Humongous Mecha. If the good guys come from The Kingdom, the bad guys come from The Empire. If the hero has an average-sized Cool Sword, the villain has a BFS. At the climax of a Speculative Fiction work, the villain may go One Winged Angel to increase his size and strength. In High School settings the local Alpha Bitch tends to be taller than the Cool Loser heroine (and she usually wears heels, so she tends to look even taller). The list goes on and on.

This is the reason why Large and In Charge is more common among villains.

Anime & Manga

 * In One Piece, most of the evil guys tend to be veritable behemoths of muscle or fat, or at least very tall and imposing. Our heroes, except for Franky and Brook, are average sized.
 * Bleach. Almost all Soul Reapers are human size, while most hollows are larger than human size (some of them are a lot larger than human size.
 * Many Arrancar hollows have Resurreccion forms that are much larger than their normal human-like forms.
 * The climactic battles Goku faces against both Demon King Piccolo and his Reincarnation namesake in Dragonball involve the latter supersizing themselves - and Goku wasn't all that big to start with.
 * In Mobile Suit Gundam The Federation focuses its resources on producing one kind of mobile suit. The Principality of Zeon, in contrast, squanders its resources on the construction of a number of huge mobile armours, including the Brau Bro, the Elmeth, and the colossal Big Zam (itself piloted by seven-foot tall Admiral Dozle Zabi).
 * In Mobile Suit Zeta Gundam, the Titans are the ones who build the Psyco Gundam and the Psyco Gundam Mark II, both of which stand the height of a small skyscraper. Those mobile suits designed by Paptimus Scirocco, while not as huge, still tend to be larger than average, with his final ride, the PMX-003 The O being a hulking Lightning Bruiser taller than any AEUG mobile suit and two or three times as wide.
 * In Mobile Suit Gundam SEED Destiny the Destroy Gundam is put into action by Blue Cosmos, the coalition of racist groups behind the Atlantic Federation. An Expy of the aforementioned Psyco Gundam, the Destroy is a walking Weapon of Mass Destruction that burns its way across Eurasia before being halted in downtown Berlin.

Film

 * Star Wars has Darth Vader, who stands over 2 meters. (though the good guys have Chewbacca, who's even taller) The Empire also has much larger war machines; the largest Rebel ship, the Mon Calamari cruiser, is absolutely dwarfed by the largest Imperial ship, the Death Star.

Literature

 * Sunday, from The Man Who Was Thursday is described as "too big to process." He's not more than eight feet tall, however, but his terrifyingly jolly personality can't possibly hurt...
 * Gregor Clegane from A Song of Ice and Fire, AKA "The Mountain that Rides", known to some fans as "The Mountain that Rapes", possibly the worse ordinary human in the series, and also the largest.
 * In Redwall, Vermin are invariably larger than Redwallers, though badgers tower above all others (and are good guys).

Live Action TV

 * In Stargate, bad guys always have big armies, big ships, big empires, and big egos.

Tabletop Games

 * Most of the factions in Warhammer and Warhammer 40 K are taller than humans: the Elves / Eldar, Orcs / Orks, the forces of Chaos (especially Khornates), Lizardmen, Kroot... An exception in 40K is the Tau, who are shorter and less physically capable than humans (which is why they prefer to shoot their enemies from miles away) - but by the standards of the setting, they tend to be a bit nicer than humans. The Skaven are also smaller but have far, far greater numbers... and definitely count as evil.

Video Games

 * Ganon of The Legend of Zelda is always bigger than Link and Zelda combined. Even in his human form, he can be up to twice as tall as them.
 * The fact that Ganon is an adult while Link and Zelda are children in most of the games could somewhat account for this.
 * Being 7 and a half feet tall probably helps too.
 * Archimonde in the final level in War Craft III is far larger than any other unit and is basically invincible. In addition, all the demonic units have far more health than the player's units or his computer allies', are physically larger, and do "chaos damage" which is resisted by none of the armor types.
 * In Infinity Blade, almost everything is bigger than you, except the final boss.
 * M. Bison of Street Fighter is a man of very large stature.
 * In the 2D Final Fantasy games, enemy sprites were always bigger than the player sprites.

Western Animation

 * Justified in the various versions of Transformers, as most of the Decepticons tend to favor larger military vehicles for their alt-modes as opposed to the smaller civilian vehicles favored by most of the Autobots.
 * One exception is the movies, which in attempt to keep a realistic scale, lead protagonist Optimus Prime (whose alternate mode is a HUGE truck) to be taller than most Decepticons.