Try ammunition cases. Seriously. I have a jillion perfume samples, and that's how I store them. I love them because they are super-compact, very stackable and hold everything nicely upright. They come in flip-top and slip-case versions, with room for 50 or 100 vials.
You can of course also organize them and label them to your heart's content.
They're not super-pretty, if you're looking to display them, but if you get the slip-case version, you can just place the bottom portion into a nicer box, so at least you'll get the benefit of having them all equally spaced-out and standing up.
You can buy them in sporting goods stores that carry hunting equipment, or online - just google ammo or ammunition cases/boxes and you'll find a bunch of sites. Cabela's is a good place.
For the 1 ml sample sizes, I recommend going with cases designed for .44 mag/.45 colt/.41 mag/.44 spec ammo. (With the MTM brand, the code would be P50-44-41 if you're getting the 50 slot version.)
You can also try the kind for .38 spec/.357 mag, but the holes are smaller and just a fraction shorter. I find the lid is a bit too snug. (Not as much an issue with the slip-case.)
Here you can see the comparison between the two sizes - the .44/.41 is on the left, the .38/.357 on the right.
If you're near a sporting goods store, consider going in with a few different samples and trying some cases out. I did that - got some strange looks, but the guy at the counter was very accommodating, if amused.
Flip-top cases for 50 rounds (or vials) -
http://ca.wholesalesports.com/storef...prod78013.html
Slip-top cases for 50 rounds -
http://ca.wholesalesports.com/storef...prod78106.html