One of the few complaints we ever hear about Dropbox is the need to store stuff in the My Dropbox folder in order to sync it. While you can work around that problem with some command line trickery, reader Nicky got good results by using Microsoft's SyncToy utility in combination with Dropbox.
As Nicky explains:
I have an e-book library which I wanted to be accessible to me via the web, but because it is managed by my e-book software (Calibre) i didn't want my default library folder to be within the 'My Dropbox' location. So I installed Microsoft SyncToy and set up my native ebook library folder to be synced/copied to a folder in the My Dropbox location
Given that e-book files aren't large (and modern hard drives have plenty of space), this is a clever way of ensuring you have web access to files but don't need to mess with other software settings. Thanks Nicky!