Can Spaces be configured by project, rather than by application?
What I've done to achieve this is to simply not assign any applications to any special space at all. That way, when opening an application, it opens on the space I'm curently on, letting me organize my work into different projects as I want.

On Lion, the organization is kept through reboots, at least for some applications. 

There is also the utility Moom, which lets you save configurations of different application windows to easily recreate spaces you use often.