The entire LA-MSS débacle. That came about because suspicions were aroused by their locking out the podium in the Vuelta a Asturias, and then one of their riders (Bruno Neves) dying of cardiac arrest on the bike in a race later that month. The police raided, found all manner of products, and banned and/or disciplined nine of the team. Not a positive test between them. And a few of the team were Puerto guys in exile, like Zaballa, too.
The fact that Rubén Plaza has never tested positive and there's no dirt on him in the eyes of the ruling bodies always has me shocked too.
All of the passport violations riders never failed a test either, so De Bonis, Lobato, Serrano, Pellizotti, Valjavec and Rosendo all go under this category.