Check out org-mode. Handles todos, scheduling tasks, timers, you can link directly to a file or an email (not a copy, but a link emacs follows into your mail reader, such as mu4e/gnus/wanderlust, for that specific email). It will auto generate an agenda from multiple todo files spread across your filesystem.
http://orgmode.org/worg/org-tutorials/orgtutorial_dto.html
There are some mobile apps but I've never used them.