The Humble Crate
Crates, as covered in Webster 1913's second definition below, are, I'm sure, very useful and convenient things to have around if you want to store or transport large quantities of fruit, weapons, or other saleable items. In the realm of video games however, crates have become virtually ubiquitous- far more common than in reality, and in turn, far more important. Any environment that could, by some stretch of the imagination, have use for a crate (and many that couldn't) will, when modelled in a game, have as many crates lying around as the designers can cram into memory.
Where to find them
Obvious habitats for crates include warehouses, museum vaults, archaeological digs, military bases, harbours, markets, garages, research outposts, cargo ships, castles, alleyways, stockrooms, and space stations. Crates can be either neatly arranged or scattered (tastefully, in varying sizes) around a room, although there are seldom any indications as to how they got there or why they were left there in the first place.
Crates appear most frequently in first person shooters, 3D action adventure games of all kinds, platform games (both 2D and 3D) and occasionally beat-'em-ups. (Oh, and console RPGs, where they're often used in sliding block puzzles. I'd better mention Sokoban as well I suppose.) They are most commonly made of wood or metal. The styling of the crate can often be used as a rough indicator of the period in which the game is set. (Metal: future; dark-coloured wood: medieval; light-coloured wood: modern; eagles and swastikas stencilled on the side: World War II.)
Useful and stylish
So why are crates so common in games? The first reason is that they can be used as a container for items that the player character will need to acquire regularly during play- ammunition, armour, and health-restoring power-ups. Access to crates is almost always gained by destroying them rather than simply opening them, but this never has any ill effects on the contents.
But what about the huge number of 'indestructible' crates that can't be opened?
To clarify this, we need to look at the crates' geometric properties. Firstly, crates are traditionally cuboid. This means that they can be represented with six sides (or often five or less, if the crate is on a flat floor, abutting a wall, etc.), making them the trivially easy for artists and level designers to model (you could even use the same texture for each side), and computationally cheap for games to render. (Modern games often use rather more detailed models to represent their crates, but they will still be comparitively trivial, compared to modelling, say, a tree, a sofa or a car.) Better still, no one is going to complain about crates looking too similar, so you can have hundreds or even thousands of completely identical ones.
Secondly, crates can pretty much be any size (the minimum probably being 1 ft. to a side, and the maximum being probably larger than a man, although beyond a certain size they become freight containers), and they can be stacked in a variety of ways. These useful properties are best illustrated in one of the first major uses of crates in a 3D game, Id Software's Doom (specifically level E2M2). Crates are used in a warehouse area, basically as 'giant lego bricks', acting as the walls of a small maze, with crates of different sizes stacked to act as makeshift 'stairs'.
An extension of using crates as 'realistic' platforms is the invention of the moveable crate (sometimes a barrel). This is one crate in an area that can be pushed into place and then climbed on to reach an objective (just like that experiment with the chimpanzee and the banana in a high place...). This 'special' crate will usually look slightly different, will be indestructible, and will be conspicuously placed in the centre of the room. (Good examples of this game mechanic can be found in Hexen II and Deus Ex.)
Inevitably, after a while people began to cotton on to the fact that crates were being increasingly used as a lazy, clichéd crutch to fill empty rooms and build simple jumping puzzles with the minimum of effort. Old Man Murray (see below) highlighted the commonality of crates (and later, cowering scientists and sewers) in games, and even went so far as to use crates as the basis of an empirical test that could be used to extrapolate the overall quality of game.
This test, known as the Start to Crate (StC) time, measured the length of time between entering a new game and being confronted with a crate (or barrel)- the shorter the time, the worse the game. Heretic 2, Messiah, and Doom all score a StC time of zero seconds, the opening scene of each game placing the player with a crate in his field of vision.
Even in these enlightened times, the golden age of the crate is far from over. Deus Ex: Invisible War, Doom III, and Halo 2 (three of the most eagerly anticipated games of the next year or so) are all pretty much certain to feature crates- prettier crates, but still likely to be ones that conform to the bizarre crate-logic of yore.