We can't see in the heads of committee members, but to understand the tradition of "what for what" in Nobel prizes, I think it is instructive to see the chain of Nobel prizes awarded for developments connected to nuclear magnetic resonance (NMR).
Here's a list. There were three prizes in Physics during 1943-1952, two prizes in Chemistry during 1991-2002 and one prize in Medicine/Physiology in 2003. The first prize was unarguably for fundamental physics, but the other ones could be argued to be "mere" brilliant experimental methods in material/chemical/bio- physics. The key to the assigned area seems to be in the usefulness for the particular area.
There is a certain point from which new developments in NMR stopped bringing anything new to fundamental physics but became extremely useful for chemistry and that is the moment the Chemistry Nobel prizes started to be awarded. Using a lot of clever ideas and commitment to use the method for medical imaging might be considered to be "just" more physics and engineering, but the invention of Magnetic Resonance Imaging is just so awesome that it deserves a Nobel prize for the area it contributed the most.
Moving to the 2014 Nobel Prizes: the mentioned fully elucidates the Nobel prize for chemistry. The development of the super-resolved fluorescence microscopy is the biggest breakthrough for chemists, biochemists and biologists. Macromolecular physicists might also benefit from this invention but not so much as the aforementioned.
On the other hand, if we simplify it a bit, the blue LED development/discovery consisted mainly of growing crystals in just the right way. The important thing is that chemical reactions were not a part of the process and thus the whole development process can be unambiguously classified as material physics or material engineering. So it's not Chemistry, Medicine, Peace or Literature. The last part of the puzzle is Alfred Nobel's will:
...which shall be annually distributed in the form of prizes to those who, during the preceding year, shall have conferred the greatest benefit to mankind. The said interest shall be divided into five equal parts, which shall be apportioned as follows: one part to the person who shall have made the most important discovery or invention within the field of physics...
That is, the blue LED was a discovery which is directly important for humankind and it could be classified as in the area of Physics rather than Chemistry, so it was awarded this way.
(Yes, this question is OT, but I could not resist trying to answer it)