Where can I find a digital, downloadable set of papercraft skeleton miniatures (or even just a single miniature)? Please note that by skeleton I mean the animated, undead monster (not a design aid for papercraft modeling). I don't mind paying a reasonable amount of money for good miniatures.
Arion Games have a vast range of downloadable paper miniatures. Skeletons are catalogue number ARG068.
S. John Ross' Cumberland Fontworks publishes the Sparks series of paper miniatures -- the Dungeoneers set has a skeleton, anyway, among other critters and adventurers. They're Truetype fonts, and as such scale nicely. Based solely on my download of the freeware Sparks minis, the illustration quality is simple but fairly good.
Stipulated that these are printout standies, and not detailed, folded papercraft minis.
If you only want skeletons, this won't be much use to you, but Paizo (Pathfinder publisher) has a series of Paper Miniature sets. Their instructions say to print them on cardstock, but I've found they do pretty well with just paper (I just slip a penny between the bases to weight them down so a gust of wind or table bump doesn't knock them out of position). I'm personally using the Emerald Spire set, which has a set of six generic spearman skeletons early on, as well as a bone priest mini. (I'm not that far through the set, though, because I'm only making them up a level in advance, and my group is only ready to start level 2.)