Words are just that – words. They have no power whatsoever and the laws of physics do not distinguish between "good" words and "bad" words.
You speak English, which happens to be one of many thousands of languages that have developed over the centuries. There is no general rule that allows you to categorise "good" words and "bad" words. In some languages the same words mean the complete opposite - e.g. čerstvý in Czech means "fresh", while czerstwy in Polish (pronounced the same) means "old", "stale" and "bad". There are many cases where words that sound exactly the same have a completely different meaning.
Similarly "nice music" is a relative term, the laws of physics cannot distinguish between music that someone finds nice and not nice.
Music and spoken words are sound waves that can make the water molecules vibrate. However this will not change the "shape" of the molecule, a molecule that is pretty simple (H2O). Moreover a molecule doesn't really have a "shape" per say, it is just a collection of particles that keep quite close to each other and follow a certain "structure". A quote from Wikipedia:
Molecules have fixed equilibrium geometries—bond lengths and angles— about which they continuously oscillate through vibrational and rotational motions. A pure substance is composed of molecules with the same average geometrical structure.
Only isomers of the same molecule have a different structure, and they become an isomer through a process called isomerization, however this cannot be practically caused by sound waves*, especially by those caused by voice or music.
Finally it is impossible for water to "align in the wrong order". A single molecule of water is two hydrogen atoms covalently bonded to a single oxygen atom. You cannot "reorder" those atoms. When an atom is covalently bonded with another one, it means that it is sharing an electron pair with another atom. Since a hydrogen atom has only one electron, it cannot be bonded with two atoms, only one - this is why reordering is impossible, you can't have
H-H-O instead of
H-O-H - the latter is the only possible "order". It is also impossible for a water molecule to become ugly. Here is a water molecule:
Ignoring the fact that we've already established that it is impossible to change its structure, I can't really understand how a structure so simple can become "ugly".
This might be related to Masaru Emoto's claims that water can react to intentions, which can be seen by freezing water and looking at the frozen crystals - it was also based around the idea of talking to water, but focusing more on human consciousness and emotions rather than just the sound. He would even go as far as suggesting that exposing water to certain pictures would have an effect on it. However an experiment has proven these claims to not be true. Emoto also refused James Randi's US$1,000,000 challenge to reproduce his own experiment with frozen water. His claims are widely considered to be pseudo-science and to violate basic laws of physics. Moreover the experiment itself and methods used have been criticized and described as not being able to verify his own claims. Physician Harriet A. Hall wrote that "This watery fantasy is all very entertaining and imaginative, full of New Age feel-good platitudes, holistic oneness, consciousness raising, and warm fuzzies; but it's hard to see how anyone could mistake it for science."
* Some isomerization happens when molecules get heated up in a presence of a catalyst. It is therefore theoretically possible to use sound waves to heat up a substance, since sound is also energy. An average yell lasting a single second would warm a glass of water 0.00000095 degrees Celsius. It is therefore theoretically possible to heat up a substance using very long shouting (we're talking months of constant, non-stopping yelling) in order to produce an isomer of a molecule, however this does not apply to water molecules and is generally a crazy idea.