The graphics card is the tallest thing perpendicular to the motherboard. My Radeon 9100 makes the package 110mm tall. A low-profile graphics card is about half that, isn't it? Apart from the graphics card, the cpu card is about 75mm tall. And I guess you'd want to keep the area above the PCI slots clear.
When I was looking around, it seemed the smallest boxes were too small. But just pay attention to the internal dimensions, allowing for the cards, drives and power supply. The Pegasos board is about 173mm by 240mm with the backplate on a long side.
Take a look at
these cases and
these cases for fun.
-- gary_c