The short answer is yes, it can be dangerous and it will have detrimental effect on your use of the system, even if the system itself won't be affected. That is to say, other users will continue as if nothing had happened, even if your user account will be useless.
Some of the dotfiles are created when the user account is first created, meaning that it will not be recreated automatically. Lots and lots of applications depend on them, meaning that those applications will not work properly. Many applications are totally dependent on configurations. If they aren't available and cannot be created, then the application will be useless and may crash or refuse to run.
It would be similar to deleting the registry in Windows, but worse since dotfiles in Ubuntu not only holds configuration, but also holds personal data. Your databases are stored in ~/.local/share/desktop-couch/ for instance. If you are synced with Ubuntu One, then deleting that folder might also delete those databases from all other computers, including the web.
If you had provided more details about why you would want to do this, then it would be easier to give an exact answer. But if for some reason you really do want to do this, then I think this is the way you should do it: (please be sure you want to)
Only perform these steps if your home directory is not encrypted.
- Create a temporary user named "tempuser" for instance.
- Add that user to the admin group just in case.
- Log out of all desktop sessions
- Switch to another console by pressing alt+ctrl+f1
- Log in with the temporary user
- Rename your old home directory (something like mv /home/bob /home/bob.bak)
- Create a new home directory for yourself
- Set the right permissions on it.
Now you have a clean system for your user, just as when you logged in for the first time. You can start to copy files from the old home directory into the new one. Don't "cut" or move. That way you'll have the old home directory as backup if something goes wrong. Please pay attention to what you're doing. If you're logged into Ubuntu One, for instance and you replace the files that contain information about synchronized files and folders, then Ubuntu One will notice that those files are no longer available. To it, that means you have deleted them and it will synchronize those deletions across your network, meaning it will delete all those files from all your computers and on the web.
So make sure you know what every file is and what every file does. And in any case, do make a backup. There are good chances you will do something you didn't intend to do, or that something you intended to do had side-effects you didn't know about.
- Make sure your reasons are valid
- Take a backup first (I'm not joking)
- Pay close attention to what you're doing
- Write down everything you do so you can learn from your potential mistakes.