Here's an article about how to include freedom in web applications, including input from Stallman: http://www.clipperz.com/users/marco/blog/2008/05/30/freedom_and_privacy_clou...
I think Wikipedia is a good example of a good, freedom respecting web application, but it's a rare exception.
A web app could be ok for email if: 1. Email was stored encrypted in a way that only you could read it 2. You could download all your data (including meta-data such as settings, aliases, groups) and move to another computer without too much difficulty 3. You had control over your email address. You can do this by buying your own domain or using an alias provided by an organisation you trust (like the fsfe.org alias I use)