For my blog, I've uploaded all the wordpress files to the root of the domain and the domain home is the homepage of the blog. I hate having so many files in the root of the domain, just to messy. Is it possible to create a folder (eg Wordpress), upload all files into this folder and then still have the domain home as the homepage of the blog?
I don't think it is, as i'm sure if you created a new folder called Wordpress for example the new URL to go to your homepage would be www.yoursite.com/wordpress.
That is exactly what will happen. If you want to do that you do have 3 options that you can do that I can think of off the top of my head 1) Create a homepage that is not wordpress with a blog link that takes the visitor to your blog (boring) 2) Create an index.html that will auto redirect the visitor to your subdomain. 3) edit your .htaccess file to auto-forward any visitors to your subdomain where wordpress is installed to. One thing you will need to do though is keep in mind how SEO friendly the second 2 methods are. I know there is is penalties for one of the two (I believe option #2.) If you are only setting your blog up for friends though than this is a non-issue.
create a blog.yoursite.com or yoursite.com/blog then modify .htaccess to redirect to your blog. I dont see any other clean way.
Turns out you can do this, http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory Seems to be a bit of ongoing work when you upgrade your blog versions.