Junk DNA, known to biologists these days as "junk" DNA or Non-coding DNA, makes up around 97% of the human genome. These are sections of DNA which don't code for proteins.

However, not all Non-coding DNA has to be actually worthless to the cell. There are numerous functions that have been found in this "junk". For example, there is strong evidence that in Cryptomonads, the amount of non-coding DNA is proportional to the size of the nucleus. The same study also indicated that natural selection is able to weed out true junk DNA (1).

Information grabbed from the much more thorough http://godandscience.org/evolution/junkdna.html

(1) Beaton, M.J. and T. Cavalier-Smith. 1999. Eukaryotic non-coding DNA is functional. Proc. R. Soc. Lond. B. 266:2053-2059.