Dropbox – How to Check Which Files Are Currently Syncing

There doesn't seem to be a way to do this at the time. Using Windows shortcuts is one possibility to make it as though the files are located in the same folders, however, it seems like it would get a bit complicated if there are a lot of folders.

There is a feature request for this exact issue, which you can vote on.

Other features you may want to look for is the ability to watch any folder, which you might be able to use in conjunction with your file system to create a limited set of folders to sync. Another one that might help is excluding certain file extensions, this would help if all the large files are of the same type (e.g. .exe, .avi, etc.).

The best option is to roll-your-own. There is an opensource option that takes a bit of set-up, but is fairly good and does respect permissions, however, it does require you to generate everything for your clients. In any case - worth checking into:

ownCloud

ownCloud gives you universal access to your files through a web interface or WebDAV. It also provides a platform to easily view & sync your contacts, calendars and bookmarks across all your devices and enables basic editing right on the web. Installation has minimal server requirements, doesn’t need special permissions and is quick. ownCloud is extendable via a simple but powerful API for applications and plugins.

ownCloud started with a keynote by Frank Karlitschek at Camp KDE’10 where he talked about the need of a self-controlled free and open source cloud.