We use 1" glass coverslips for microfabrication, and typically store
them vertically in boxes meant for microscope slides like Slidefile Jr
shown on this page
http://www.emsdiasum.com/microscopy/products/preparation/mailers.aspx?mm=8
but admittedly the boxes are taller than they should be for 1x1", and if
you invert them, pieces fall out. Beyond that, they work well.

For cleaning work we have PFA racks from Entegris like A14 on this page
http://www.wafercare.com/Default.asp?G=57
Which are very nice, but almost impossible to buy. (They are rarely in
stock, and don't produce them unless you place a minimum order of 100 pc
  @ $100 each. If anyone has tips on how to get them, I'd appreciate it...

Martijn