The first thing we were doing was the civs, but we messed up a bit when we made a few UUs, buildings and other things. I sugest focusing a lot, and dividing the files among everyone instead of many people editing the same file. Oh, and one of the hardest parts of civ design is the diplo files; it can crack the whole mod and requires a lot of work. I sugest using regular diplo from the game (for example, make each leader use diplo from one vanilla leader - this way is good because later you can only use Find->Replace All to change all references at once), and then replace it as you make it.
I've been thinking about this as well and seeing that this is a group effort I think a Version Control System might be called for, so that we can always access and work from up-to-date files.
The ones I know from the top of my hat are:
Subversion: Good, with a lot of graphical tools for the commandline challenged. The problem is however that my webhost doesn't provide the HTTP-webdav module, so I can't provide hosting myself, but there are multiple possibities for free hosting.
Bazaar the vcs I'm used to work with. I should be able to get the repository on my webhost, but otherwise (or maybe even preferably) there's free hosting available at http://launchpad.net. I think there's a graphical interface available, but I haven't used it, so can't really comment on it.
And of course CVS itself. I haven't worked with it, and don't know what is required for hosting the repository.
I'm open to other suggestions as well (even to not using it, though I think it will help us a lot).