1. Is the code it generates XHTML compliant? If not how difficult would it be to design a site using WB and get the code to validate to W3C?
The template can be made yourself, so you can make your whole page XHTML compliant. Look for more information about this in the template forum.
2. Is there some kind of comment script module? For example, if I write an article or something and want to allow people to add their own comments about it?
You can use the news module. This has the option to make comment for posts, etc.
3. How difficult is is to use your own PHP scripts with WB? Example being if I have already wrote my own email processing script, how difficult is it to integrate with WB? I've used other CMS's that this couldnt where this couldn't be done and others where you had to literally jump through a thousand hoops to try and get something simple like this to work.
You can work with the code module. This allows you to create PHP script within your page. Furthermore you can also create a module if you have special needs. It's very easy. I have created a few and I am not a PHP developer....
I think that is all my questions for now. I'm just looking for a basic CMS for a small to medium size site where I can easily update it and allow user comments (kinda like a blog but not really)
You can also navigate to OpenSourceCMS.com
and try the demo of 'WebsiteBaker' over there. It is working very easy if you'd ask me.