I've thought about this question also.

I carry some pills loose in capsules, but most of the meds I EDC are in their original sample packaging. It keeps out moisture and makes it far easier to identify pills under stress. In the event that you wanted to give someone medicine, they are far more likely to be comfortable taking a labeled package, rather than having you fumble with anonymous pills in your hands and potentially giving them the wrong one. There are tradeoffs either way, but I'm okay wasting some space for the extra clarity.

By the way, I've ordered a bunch of sample-sized meds from http://minimus.biz/ and have been very happy with their service.