OneNote only comes with Microsoft Office. Which you can also purchase for Mac. Xcode is free. A developer code signing certificate costs money whether you buy it through Apple or Verisign. Want to release trusted apps on Windows that don't throw up scary looking security warnings to your users that download them? Guess you'll need to pay $299 a year to Verisign or some other CA for that privilege.
Gatekeeper is actually a cool feature because now any developer will be able to release signed applications without going through the app store approval process. If they do nasty things, their certificate gets revoked. You get the benefits to the user of running signed/trusted code, and the benefits to the developer of deploying for free, without app store approval.