I've seen plenty of webpages created with some sort of tool, leaving local pathes or other itneresting information inside comments, or producing pure HTML mess.

Concerning clean source code, there are not many tools you can trust.

I've switched to my own tempalte system, which means that I'm coding dynamic content with PHP, but all other stuff like the design is done by simple HTML files which even allow short injections for things like links and images.

I'll never go back to WYSIWYG again.
I prefer some tool like Phase 5.3, which is basically a text editor with additional shortcuts which produce HMTL source code. By hitting a single button, it loads the page into an integrated browser window. It also allows to configure usage of your own webserver in case you're working with PHP and/or MySQL.

That's not really WYSIWYG but it's at least YGWYRW (you get what you really want)