We use github for code hosting, issue tracking system and specs ( the wiki portion ). Dropbox for large files like designs, videos. Basecamp for collaboration and discussion coupled with real time chats over hipchat.

I bought into the appcelerator promise a while back but had since abandoned it for native development. It depends on your app but our app would look and behave significantly worse had we not gone native.

Hope this helps, call me If you need more info.