In some games, a few of the rules cover situations that only occur very rarely, sometimes only once every few game, or even few hundred games.
These fall into the following categories:
Lots of Pieces
In games such as Magic: the Gathering or ASL, there are thousands of unique components, only some of which are brought into play in a particular game. Therefore, the rules that apply to these components will only be relevant when they are present in the game.
A Latent Threat
Sometimes a rule is in place more to affect the game play then to actually be used. For instance, I've played Lord of the Rings: the Confrontation dozens of times, and not once has Merry killed the Witch King with his special ability. That's because the Dark side ensures that the Witch King doesn't blindly attack before knowing if its target is Merry.
While the specified event may occur infrequently, sometimes the rule can have a vast effect on game play.
A Hole in the Rules
In this category are rules that are added to cover unusual situations that can occur.
For instance, there is a rule in Puerto Rico that when a player uses Hospice and there are no colonists left in the supply, he or she takes on from the boat. I rarely see this happen, but it can, so someone had to come up with a rule to cover it.
Incidentally, that's what playtesting is for. You don't want your players having to guess what to do in these situations.
The naturalness of the added rule determines whether people consider it a natural extension of the mechanic or a "fiddly" addition to the ruleset.
A few games include some very rare situations simply for comic effect. For instance, in Cosmic Encounter, there is a rule that if the Big Bang and Bigger Bang moons are both revealed at the same time, the Biggest Bang occurs, and all people instantly lose the game.
The likelihood of this occurring is quite small, but if it does ever happen, it makes for a good story.