Well, I did a quick read of the link and came up with what I said in my last post, but I didn't really follow it and think about it. Now I have read it more carefully and followed some of the links. Cryptogenomicon
has a discussion of the matter with a huge number of comments following it. After reading through half or more of the comments I came up with the idea that we don't know enough to really say. In the comments there are a bunch of different ideas about what the 'junk' DNA is. Some suggest that it may not do anything directly, but it may have some kind of structural effect that influences what the active parts of the DNA do. And I think there are some other comments on what it might do.
The main thing I got out of the discussion was that we really don't know enough about how DNA works to really figure out what the junk does or doesn't do. It may be that a lot of it will turn out to be junk, or it may have some subtle effect that we just don't understand yet. In the meantime we people on the side lines will just have to wait and see what comes out of the ongoing research.