I use a Cryorig H7 in my Carbide 88r Micro ATX case, its a nice short and compact cooler, looks good as well if you care about that. Keeps my 6600K in the 60s when gaming at 4.6ghz, extremely quiet as well. Highly recommended.
Hardware Secrects say Zalman T3 has 150mm CPU clearance.
Like Daaaveee said, H7 would be a good choice. Might be hard to find one at the moment. I'm expecting much better availability of Cryorig in about a month.
Maybe Alpenfohn Brocken ECO, but many normal coolers won't fit on some mATX motherboards. Some have CPU socket quite close to PCIe socket .. and RAM socket.