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Nigiri is the big grandaddy of the sushi world—the one which'll really test your skills. It's the only one that requires any really challenging knife skills, and without the aid of a sheet of nori to hold everything together, shaping them also takes quite a bit of practice.
More likely than not, your first few attempts will leave you trying to pick up pieces of slightly ripped or frayed fish on top of misshapen blobs of rice using fingers that are coated in sticky bits of rice. It took me several weeks of nightly practice to get the rice right, and several years of knife experience before I could get it sharp enough and wield it delicately enough to get the fish into that perfectly cupped, tapered shape. But don't worry! Even the less-than-visually-stellar pieces will still taste delicious, and you'll only improve with time.
The Tough Bits
The most difficult part of making nigiri after finding the right fish is cutting it properly. The goal is to minimize the length of strands of connective tissues, while at the same time slicing the fish in such a way that it forms a slight concave shape that wraps perfectly around the block of rice.
To do this, unlike fish for makizushi, which can be cut parallel to the sides of the fish log, you must cut perfectly orthogonally to the lines of connective tissue, like this:
The knife must also be held at a 45-degree angle to the cutting board to create slices of fish with an increased surface area. Part way through each slice, the angle of the knife must be shifted in order to create the necessary cup shape. All of this has to be done in a single smooth stroke so that no visible cut lines or saw-marks are apparent on the fish. It's a real challenge, but one you'll find extra-rewarding the first time you pull it off smoothly (and you will get there with time).
While pristine, sparkling fresh raw fish are the most common toppings for nigiri, cooked items such as broiled anago (freshwater eel) or yakitamago (Japanese-style layered omelet) are common and delicious. Usually, when adding a cooked topping, it is secured in place to the rice with a thin nori belt. Just like with temaki if the topping is already seasoned (such as with broiled eel), there is no need to dip it into soy sauce before consuming.
As far as etiquette is concerned, like all sushi, nigiri is a finger food. You can use chopsticks if you'd like, but there's no need to. Pick up the fish with your fingers, and dip the corner of the fish-section in the rice (you'll have to partially invert the roll to do this without getting soy sauce on the rice). If the nigiri is well made, the fish should stick to the rice ball and there's not much danger of it flopping off and making a splash in the soy sauce*.
*I still managed to do this at dinner on Sunday
Ok—still dying for a bad pun or two? Here ya go: I once asked a sushi chef for some sea scallop nigiri and instead received some kind of white fish. When I asked him what happened, he said, "My apologies sir. It was only a fluke."