I have most of mine in those Ziploc or Glad brand containers with the snap on or twist lid. Then, they're in a deep drawer and a plastic storage bin. I store them upside down so I can see the liners through the clear bottom of the container.
When I know I'm going to need a certain type of liner, as soon as I can I jam them into container narrow enough to push up the sides, but keeping the bottoms flat. "Training" the liners like this keeps them from creasing in the pan or popping out of the pan.
I "nest" all the liners inside each other and store them in a plastic box (the kind with a snap-on lid). I usually keep the liners in their original plastic bags (even if opened) insdide the box. (Unless I accidentally throw out the bag! I won't tell you how often I do that...) 
I buy mine in bulk so they come in a tall box which is where they stay until the box is empty. But sometimes I do get like those seasonal ones that are just in a plastic bag like wilton ones etc. For these ones, an empty Pringles can works great!
pringles can!!! genius! why didnt i think of that!!!! going to try that now! i have mine in a ziploc bag but worry about them losing their shape!
Thanks for all the ideas. My dh got me some veiwtainers (http://www.viewtainer.com/) at a hardware store when he was getting stuff to fix the bathroom sink.
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