Sex chromosomes are the chromosomes which determine the gender of an organism (this only applies to an organism whose gender is determined by its genes rather than by its environment).
In humans, fruit flies, and other animals where the male is the heterogametic sex, they are the X chromosomes and Y chromosomes. In birds, moths, and other animals where the female is the heterogametic sex, they are the W chromosomes and Z chromosomes. For humans, the sex chromosomes are the 23rd pair of all chromosomes.
The sex chromosomes of most plants (when they exist) are also known as X and Y chromosomes; ginkgo trees have their own unique system of sex chromosomes.
The information in this writeup was taken from the science dictionary at http://biotech.icmb.utexas.edu/; I oversaw the development of the dictionary (the website was mothballed in 1998) and I believe I wrote the entry this is based on.