I'd prefer to have all the comments located in a single location (e.g. ~/.comments or ~/Dropbox/comments-<hostname>) rather than litter hidden files all over the place because I could (1) easily back them up, (2) share them (even across different platforms), and (3) allow multiple users to set local and global (shared) comments.

EDIT

Because I was bored: https://gist.github.com/2697095