[raphman]

The distance between the two rows of pin headers on each side is not a multiple of 0.1". This means that every shield that you attach to the Arduino needs to have this same strange spacing between the rows of pin headers. You cannot just use a normal perfboard. As all Arduino shields have the same weird spacing, fixing this design flaw would require everyone to buy new shields. There are Arduino clones that add correctly aligned rows of pin headers [1], however.

[1] http://shop.pinguino.cc/image/cache/data/olimex/pic32-otg-50... (actually, no true Arduino clone)

Edit: found a good explanation with pictures here: http://brettbeauregard.com/blog/2009/07/arduino-offset-heade...

[rcfox]

Couldn't they make an adapter?

[Pyrodogg]

Apparently a someone does. http://www.sparkfun.com/products/9374

From raphman's link