With micro ATX a lot of them come with mini PCI-e and main half height Mini PCI-e slots. Surprisingly there are TV tuner cards for them and other odd stuff in mini PCI-e size besides the normal wireless/bluetooth and ssd cards. Or you can get a Mini PCI-e card with a flexible cable to regular PCI-e 1x slot like this. http://www.amfeltec.com/products/minipc ... dapter.php
Converts MiniPCI Express bus into x1 PCI Express with a Flexible connection between MiniPCI Express host card and x1 PCI Express adapter board. If you have space in your case to put the full sized card .
With Matx and atx boards All the smart board designer's put a PCI-e 1or 2x slot on top of the 16x slot and in slot 3 the second slot under a PCIE16 x slot then you at lest have one to two Unobstructed 1x slots. The second example is usually when a SLI/crossfire board is made to hold triple slot graphics cards.
Triple slot graphics cards are dumb...I could see a dual chip card using 3 slots but a single chip card its so unnecessary.
Asus makes triple and double slot single core graphics cards and the triple slot cards are no better then the double slot cards.
Now that i Think about it I have yet to see a dual chip 7990, 590, 6990, 690 card made in the triple slot design....and that's where it would make perfect sense for bigger coolers on each chip so they would not have to be downclocked to stay within thermal limits.
If anyone has seen a triple slot dual GPU card let me know.