The Human Genome Project was only a start, and it concentrated on the part of the genome which codes for proteins known to be used. This amounts to 2% of your DNA, and the amount actually active at any particular time may only be 1%. A project named ENCODE went much deeper in trying to find out what was going on in the "junk DNA".
There is a great deal of controversy about what constitutes functional DNA. Some of the higher figures quoted are 80%, and even the possibility this will ultimately turn out to be close to 100%. There are critics who claim the whole project was mismanaged from a scientific standpoint, and the result should be much closer to earlier estimates.
What gets overlooked in the controversy is that even the critics are saying that 9% of the DNA is active and functional. Depending on what you consider the previous percentage of non-junk DNA to be this could be 4.5 or even 9 times earlier estimates. This is a huge gap in our understanding.
If you can find a match with some known problem you may save a life, and
Stephen Kingsmore has done just that with technology that can sequence the whole genome of a sick infant in less that 24 hours. I've read that he was able to identify the genetic disease in 28 out of 44 cases, and could recommend a treatment in 14 cases. Perhaps 5 infants have been saved so far as a result. Unfortunately, this is still a minority of cases.
We are still very much in the dark about what a lot of this genetic material is doing. I'm working on a blog post on what has been discovered so far. A great deal of our understanding of basic human biology is in the process of changing, and I really wonder how the medical profession is going to deal with this.