You can use all of PHP's built in functions in RoundCube, you can read about them at PHP: PHP Manual - Manual you can also use any JavaScript in RoundCube I recommend use jQuery because RoundCube already uses it. The theme documentation hasn't been made yet, the best way to learn about it is to look at other plugins.
By PHP functions, I actually meant Roundcube's own classes/functions like e g html_inputfield and get_input_value. Sure, there's an API, but no real examples on how to use any of it. If you're developing under a "framework", you want to follow it, otherwise it will look like you write poor code. Right now I'm using my own database class to manage things cause I cannot find information on how to use Roundcube's own.
I'm also looking for information about handling the $args['blocks'], which types it supports e t c. I'm writing a small plugin to be displayed in the user preferences and I really find it cumbersome to use somewhat complex PHP-classes to get a simple HTML written out. A tutorial on this would be invaluable for someone like me!
Thanks for the support so far though!