I looked up for other solutions which allow this (for example by doing the encryption separately for each file; but I could also think about other things).
I only found http://www.arg0.net/encfs so far but I didn't tried yet. It does the encryption separately for each file.
http://news.ycombinator.com/item?id=895660
Dropbox supposedly encrypts server side. If you want to encrypt client-side, use SpiderOak or TarSnap. These hacks on top of Dropbox don't mesh with the semantics of Dropbox properly and will cause problems days, weeks, or months down the line unless managed extremely carefully.
EncFS is somewhat better in terms of sync, because it encrypts each file separately.
Here's a nice tutorial: http://pragmattica.wordpress.com/2009/05/10/encrypting-your-...
I have ~2.5GB of encrypted files in my Dropbox, and as long as I don't try to edit the same file in two places at the same time, it works like a charm. (Conflicts can be nasty, as another comment says. But it's not as bad as TrueCrypt, because EncFS works per-file.) Editing different files at the same time, on the other hand, is kosher.
There are, however, a few other problems with EncFS.
First of all, you can't mount an EncFS directory tree from Windows. There's an actively developed Windows port of EncFS out there (which uses Dokan), but I've never been able to get it to work properly.
Also, Windows has a maximum path length limit of 260 chars. Since EncFS pads file names with unique IVs and base64 encodes them after encrypting them, you can reach this limit after only 3-4 levels of subdirectories. Paths which are too long for Windows will simply be omitted from the Windows copy of your Dropbox folder. So if you ever treat the Windows copy as an authoritative backup, you're in for a nasty surprise. Linux is OK up to 4096 chars. I'm not sure how OSX does it.
Lastly, Dropbox in Linux tends to choke when you add a large number of files with encrypted filenames. It's not uncommon for Dropbox to declare a "case conflict" in that situation when there actually isn't any case conflict. This can seriously damage your EncFS directory tree, because Dropbox adds the phrase "(Case Conflict 1)" to random files and folders. An easily solution is to stop Dropbox, add the files, and restart Dropbox again. But this can get annoying after a while.
http://msdn.microsoft.com/en-us/library/aa365247%28VS.85%29....
I know that not all software supports those long file/path names, so yeah, you are probably in for some surprises.
In combination with some (really simple) bash scripts for mount- and unmounting, this is imho a good way to encrypyt files inside your Dropbox.