My original problem is that I have a directory where I write various scripts. Each of them is independent of others, and usually one-file-long. I want to have some versioning ap
How about a compromise between 1 and 2? Instead of a folder+repo for each script, can you bundle them into loosely related groups, such as "database", "backup", etc. and then make one folder+repo for each group? Then if you clone a repo on another machine, you're only pulling down a smaller number of unrelated files. (Is the bandwidth/drivespace really a concern?) To me, this sounds WAAAY simpler than all of the other suggestions so far.
(Technically this approach meets your requirements because (1) each script isn't in its own directory, (2) not all scripts are in the same repository, and (3) you can easily do this with any popular DVCS. :D)