Bore and stroke
The bore is the diameter of the cylinder, the stroke the vertical distance between the highest and lowest points in the piston's travel. A shorter stroke usually allows higer revs.

Compression ratio
When the piston is at the bottom of its stroke, the volume above it is the total volume. When it's at the top of its stroke, the volume is the clearance volume. The ratio between these two is the compression ratio. An engine with a higher compression ration will squeeze its fuel/air mix harder and create more power.

Fuel system
Fuel injection squirts fuel into the cylinders with nozzles. Carburettors use the suction effect of air entering the cylinders to draw a fine mist of fuel through a hole. The throttle moves a tapered needle in and out of the hole, controlling its size.

Six-speed gearboxes with a chain final drive are the norm. Lazier engines with a broad spread of power may use fewer ratios (a Kawasaki ZRX1200S has five), but peaky, high-revving engines with narrow powerband need more (a 125cc Cagiva Mito has a seven). Belts are cleaner but less durable. Shaft drives are cleaner and maintenance-free but heavy and bulky.