After some sweat and tears I got it working as it should. At the moment the file structure looks like this:

Code:
.
..
root.htm
root.py
/functions/.
/functions/..
/functions/functions.html

And as you can see, no matter what HTML file you try to get to right now, you will end up triggering root.py.

Examples:
http://www.userjs.noteme.com/root.html
http://www.userjs.noteme.com/functions/functions.html
http://www.userjs.noteme.com/penagate/cheersm8te.html

But non html links will still look for a file:
http://www.userjs.noteme.com/root.htm


So I guess I am happy, cheers,
- ØØ -