Solution: stylish lacquered boxes. I've been looking for ones that will fit 8 1/2 x 11 paper and I've finally found them! Several of them in fact! Below, are various sizes of boxes and sources.
White/Black Stacking Lacquer Boxes, $64-$108, from lille a shop
Duck Egg/Sand Stacking Lacquer Boxes, $64-$108, from lille a shop
Pink/Chocolate Stacking Lacquer Boxes, $64-$108, from lille a shop
Distant Origins Lacquer Stationery Box, 9.5"x12.5"x2.5", $145 at Vivre
Barneys has a very similar white version as well for $135, Barneys New York
Laquered boxes and trays, $45-$130 at Vivi
Tri-Blue Collection, $72.50 -$92.50 from JayJayDecor
Bodhi Leaf White Stationery Box 12.5"x9.5"x2.5", $122.50 from JayJayDecor
Dragon Fabric inlay with lacquer 12.5"x9.5"x2.5", $122.50 from JayJayDecor
Computer Disk Box, 5.25"x3.75"x6" at Envie Home Decor
Set of 3 Black Boxes, $265 at Instyle Decor
Set of 3 Espresso Lacquered Boxes, $295 from Plantation Home (additional styles and trays available as well)
Macassar wood jewelry box (but could be used for desk organization, don't you think?) $495 at Williams Sonoma Home
Marquetry Boxes, $108-$148 from Williams Sonoma Home (coordinating trays available as well, $168-$198)
Pacific Connections seems to be the source for several of these and even offers Bath Accessories!