Depending on how deep you want the integration, there are several options:
1. For look and feel: create a custom theme and modify the CSS to fit in with the rest of your site.
2. For navigation: use an advanced custom theme and insert navigation links at the top or bottom as you see fit: http://www.question2answer.org/qa/704/how-can-we-add-one-more-tab
3. For user management: implement single sign-on, as documented in qa-external-users.php
I realize all of the above requires work, but it's not really technically viable to integrate with existing websites in any other way (unless they're running a standardized platform such as WordPress, in which case hopefully a future version will make this integration much easier).