Note: this answer was written a long time ago and no longer applies to modern Windows version and currently supported software.
Since encfs is built on top of fuse, the obvious way would be to port it to a fuse driver for Windows. Apparently the two most likely possibilities are Dokan and Eldos Callback Filesystem, though neither currently advertises encfs support.
In the meantime, an alternative would be to run a tiny Linux file server inside a virtual machine or with Colinux.
An encrypted filesystem that is supported by both Windows and Linux is Truecrypt. Synchronization via Dropbox is likely to be a lot more expensive than with encfs, but it might still be doable if your files are small enough.