Find first pin of a LQFP chip
If you have multiple circular indents on the package, and they are all the exact same size and shape, then they are not the identifying indents.  In that case the identifying dot will be printed.

In general, though, you have 2 types of indent in the package.  Large flat ones are part of the moulding process and are to be ignored.  The identifying one is usually smaller and deeper - often with a more concave profile to it.

For instance, take this chip from Creative:



The larger dot in the upper right is a moulding artefact - the one in the lower left is smaller, and they have even gone to the trouble to accent it by drilling a further hole in it.

This one from ITE is more tricky:



Both the dots are the same size and the same depth - however the lower left one has a small bar across it - not easily visible to the naked eye - which highlights it as the identifying corner.

This one is more akin to the Atmel:



You can see the two dots are different sizes.  The identifying one is the smaller one of the two.  The larger is the moulding artefact.

So in summary: 


Large and shallow = not it.  
Small and deep, concave, or otherwise not just plain large and shallow = it.