Cemetary and graveyard are interchangeable, they are both burial grounds for the dead. The only difference is that graveyard may have a second definition:

A place where worn-out or obsolete equipment or objects are kept: an automobile graveyard

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Let's see what Webster's says:
cemetery : a place )(0ther than a churchyard) where the dead are buried. from Gk koimeterion, sleeping place.

graveyard : a burial ground, a cemetery

Looks like they are synonyms

a cemetery (from the Greek for sleeping place) does not belong to a church,
a graveyard (from the Danish & Icelandic: cut and enclosed place)might belong to a church
in their uses, cemetery is more often used to refer military cemetery, (where there is little or few engraved stones) and the space cannot be called a yard anymore. Graveyard applies mostly to small cemeteries.

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Note added at 13 mins (2004-04-04 16:21:30 GMT)
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also, as graveyard refers not only to human burial but also to over objects as Aaron explained

This is a subtle difference.

The term "cemetery" is normally used to refer to a place that is designed to be a money making enterprise. It refers to a place like Forest Lawn, for example, where the grounds are kept in a very nice and beautiful condition. A "graveyard" on the other hand, may or may not look nice. At one extreme, it might be a mass grave like Hitler used for his massacres. At the other end of the spectrum, it could refer to a small cemetery that has fallen into disrepair. In general, however, the term "graveyard" indicates that proper respect for the memory of the deceased is somehow neglected.

Sincerely,

Arthur