I recently suggested that links in task item notes should open in new windows, or at least they should add the option to choose that behavior. Toodledo responded that they originally had this, but some people wanted every link to open in a new window, while others wanted subsequent links to recycle the new window. With both camps complaining, they just removed targets from the links altogether.
Anyway, here are two bookmarklets for Toodledo. Clicking these will modify the task note links to open in a different window.
Note: You will need to click this each time you load the page, or add a new item. Yes it’s clumsy, but this is only a band-aid until Toodledo adds the feature.