I use glass jars for all my pens, pencils, paintbrushes, x-acto knives, colored pencils, markers, etc. with only like stuff going in each jar. They're lined up all neatly and it's easy to find stuff.

Incidentally, B&G pickles make great ones ... they have nice sizes and the jars are plain ... no brand imprint, etc.

At conferences everybody gives out logo mugs. Lined up on a shelf, they make great holders for pens, staples, rubber bands, etc.

I use an old silver creamer pitcher to hold my pens on my desk.

i hang them on a piece of string :)
(only works for pens and mechincal pencils, with the "shit pocket clip")

hahahaha... SHIRT pocket...

I bought the IKEA BYGEL kitchen storage rails and containers for a kitchen with limited storage space, but when I moved I didn't need it in the kitchen anymore so i hung it over my desk and it holds everything from pens to rulers to spray mount.
It also looks really cool!Here are the links to what I have:
Rail:
http://www.ikea.com/us/en/catalog/products/50072645
Cutlery Caddy:
http://www.ikea.com/us/en/catalog/products/10072647
Containers:
http://www.ikea.com/us/en/catalog/products/00115732
Wire Basket:
http://www.ikea.com/us/en/catalog/products/90072648

I wondered about the first comment antimatt !

I had never heard that one before!

i use old cups & glass jars, but my favorite is the yahtzee dice cup. (i [insert heart here] yahtzee & the dice & scorecards disappeared years ago.)