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In the "Editing" panel (F9), box "Mesh tools", there is a setting named "Limit" : the tiptool is self-explanatory : "Specifies the max distance 'Rem Doubles' will consider vertices as 'doubled'". The default value is 0.001, this is expressed in Blender units.
Another useful option is Alt-J while in Edit mode : this feature tries to converse triangles in your mesh to quads. As an example, try to convert a cube to a triangle-only mesh (Ctrl-T) then using Alt-J will get you a cleaned mesh.
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