I had to cut the drive carrier a bit so that the cpu card has enough room (otherwise the carrier would be sitting on top of the cpu card). For this case you have to use the included riser card to use gfx or other cards (no need for low profile cards). But I had to fix the agp riser card a bit because it was for AGP x8.
Here is a picture of case loaded with Pegasos board:
http://www.pegasosforum.de/album_showpage.php?pic_id=124