Azumanga Daioh (a box set of 5 DVDs)
While they're not exactly what I'd call "box sets," there're also:
Girls und Panzer (3-DVD case), which should almost certainly be paired with the Girls und Panzer OVA DVD (in a separate case)
Girls und Panzer OVA 7 and Girls und Panzer der Film both come in cases that hold a DVD and a Blu-Ray
Dusk Maiden of Amnesia (3-DVD case)
Maoyuu (2-DVD case)
The Aria series (1 4-DVD case and 3 5-DVD cases)
While they're not exactly what I'd call "box sets," there're also:
Girls und Panzer (3-DVD case), which should almost certainly be paired with the Girls und Panzer OVA DVD (in a separate case)
Girls und Panzer OVA 7 and Girls und Panzer der Film both come in cases that hold a DVD and a Blu-Ray
Dusk Maiden of Amnesia (3-DVD case)
Maoyuu (2-DVD case)
The Aria series (1 4-DVD case and 3 5-DVD cases)
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"The Lady of the Lake, her arm clad in the purest shimmering samite, held aloft Excalibur from the bosom of the water, signifying by divine providence that this was some killer weed."
"The Lady of the Lake, her arm clad in the purest shimmering samite, held aloft Excalibur from the bosom of the water, signifying by divine providence that this was some killer weed."