[hemicyclium]

There has been renewed interest in finding out what non-coding DNA (aka 'junk' DNA) actually does. Some prominent theories are that some kinds of non-coding DNA are epigenetic controls, but there isn't a complete set of theories yet. There ARE transposable elements, sequences of DNA that can essentially move around in your genome at will, and cause problems by doing so: imagine getting a transport protein sequence in a stem cell cut in half. Even then, these are kind of like DNA parasites, not junk.

[coriny]

Sorry, I'm going to nit pick, but non-coding and "junk" aren't the same thing:

Non-coding just refers to not being translated to protein, and we know (as you list, more for the benefit of others) that there are many non-coding functional elements.

Junk DNA is non-conserved DNA (e.g. shows only neutral selection). And if it's not being selected for or against, then it probably doesn't have much effect either way.