When you die the world resets a bit and it does not always remember certain things. Overall I would say just that there are no negative effects to your character but it can be very inconvenient.
For example, you will not always reset to where you were. This can cause things you had before in the environment to no longer be available. I can not express how many missions I have had be made harder simply because it reset me to a location not only without the vehicle I had with me, but without any vehicles nearby at all.
That does appear to be the extent of the changes though, strictly just the environment getting reset. Your money, reputation, player equipment and experience are all still intact.