I hacked a User-Javascript which adds Markdown support to the Notebook section. Sadly I havent been able to get anything working for the nodes attached to each task, so feel free to contribute if you have any idea.
DISCLAIMER: As the script modifies the page it may brake the page on any improvment to the page performed by Toodledo or by any browser change. Therefore I highly recommend not to try it unless you have a working Toodledo backup strategy and trying it on some dummy notes first. In case of errors first try visiting Toodledo with the script disabled.