Supercomputers are ordinary computers, just more powerful than "normal" computers. One has to realise why they are more powerful.
In one type of supercomputers -- considered as the real supercomputers by public -- it is because their processors are much faster in computing some exact operations. In particular this is the case of vector supercomputers that are able to process whole vectors (n-tuples) of numbers at a speed of normal processors working only with scalar operands (separate numbers). Nevertheless we don't have a vector supercomputer in MetaCentrum yet.
Generally, the supercomputers needn't have faster processors than are available in PC's or simple servers, but they have a lot of these processors. That has a fundamental impact on which problems supercomputers can compute faster and which they can't.