Merle

Merle in heterozygous form affects only eumelanin, not phaeomelanin. It looks similar to a partial dilution of these areas. The amount of merling that will takes place can vary heavily. Dogs with very little merling visible are often referred to as minimal merle. Sometimes a puppy may be born that is genetically merle, but with no merling visible at all. Yet when bred, these dogs can produce merle puppies. These dogs are referred to as cryptic merles or phantom merles. It is important that these dogs are properly registered as merles, to avoid unintentionally producing double merles (see further below) when breeding.

Different merles
The most common type of merle is black plus merling, which gives blue merle. Merling on liver is also not unusual, and referred to as red merle.
While blue and red merle is the most common, merling can also affect blue and isabella. These merle forms are often referred to as slate merle and isabella merle or lilac merle respectively.

Most merles typically seen are solid in colour, or tanpoint, but merling can appear on any pattern. On some patterns it will be more visible than others. Merling can also appear on a recessive red/cream dog, but since these dogs lack visible eumelanin pigment in the coat, no merling will be visible at all on them! Sometimes you can tell that they are merle, however, from looking at their eyes and nose.

Eyes & Nose
The merling can affect not only the coat but also the nose and/or eye pigment. When the merling hits the eye/s, it causes them to become blue rather than amber/brown. It can affect part of or the entire eye.
When it affects the nose, it will likewise leave pigment-less spots. These will be pink in colour. Such a nose is called a butterfly nose.

The problem with double merles
Merle is a dominant gene. The description on this page is for heterozygous dogs. Homozygous merles are called double merles. They are also sometimes referred to as for instance lethal white although this is actually a horse term, and refers to a pattern in them that originates from different genetics. 
The double dose of merle produces mainly white dogs that often have hearing and/or eye problems, sometimes they are even born without eyes. Many breeders disagree with producing double merles intentionally and some kennel clubs have banned such practices. Double merles appear similar to normal merles, but are usually heavilly patterned with white, and a few remaining merle patches. Such a dog should, however, not be mistaken with a 'regular' merle that is also patched with white.
Go here to see examples of the health problems that can be found in double merles.

Harlequin
The pattern harlequin as it is found in great danes (beaucerons are sometimes called harlequin too, but then it is used for regular merle) is a tricky pattern. It is not known for certain how it is formed, but it may be merle combined with another gene that is not yet mapped. Harlequin usually works on black but there are also so-called porcelaine great danes (in the USA these dogs can be called brindlequin, fawnequin etc) that are harlequins with non-black based colours (such as brindle or fawn). These dogs look spectacular but cannot be shown in dog shows. They may be more prone to health problems than other colours.

Go here to see how sable merle can develop in a shetland sheepdog.

Blue merle border collie puppy. Note the pink nose spot and blue in the eyes. This is caused by lack of pigment in these areas - a result of the merle gene.

Red merle dachshund.

A sable merle catahoula leopard bitch with a litter of puppies including blue merles and sable merles.

An australian shepherd puppy that is sable merle, and also masked. You can see the dam, P.C, here, and she appears to be a double merle. 

Blue merle (with tan points) and white (piebald). This particular dog is not a double merle, but it has a similar appearance to one.

Double merle border collie. These dogs often have eye- and or hearing problems, and the intentional breeding of them are banned in places.

A harlequin great dane. The similiarity with the merle pattern is striking, but harlequin has a much lighter base colour.