My study area is surrounded by windows. There's not a lot of space for storage. I solved some of the problem by using bathroom accessories, designed to suction onto tiles or glass. The top photo is a soap rack, that nicely holds my PDA and phone while they're recharging. The stick-on hook helps keep my cords where I need them, instead of all over the floor. The bottom picture is a basket, I guess it's really designed for toothbrushes or razors or so forth. But it makes a jim dandy pen holder.
You do have to be careful, particularly with things with cords, that you can still easily open and shut the window. Make sure to stick your bits and pieces on the sliding half of the window!
And an extra tip - if the suction caps don't work very well (you have no idea how often my phone and PDA ended up on the floor!) put a little bit of vaseline around the outside edge of cap (leave the centre clear). Works a charm.