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The first suspect in the Case was the one from the Tanner-Sighting. The second suspect is the one from the Smith's Sighting. He is still the main suspect in the case.
The third suspect was Robert Murat. He was cleared to be innocent by PJ.
The fourth suspects were the Parents McCann. The issue is hold on ice.
There were several intermediate suspects since from alleged suspicion. See e.g. the Tanner-Sighting or the Rasta-Man
The actual suspects can be found at Operation Grange.