I use (and abuse) [[http://taskwarrior.org|TaskWarrior]] and [[https://github.com/ValiValpas/taskopen|Taskopen]]\\
Some examples of use:
  * Adding a task<code bash>task add ExampleName</code>
  * Display the list of tasks<code bash>task</code> Output <code bash>ID Age Project             Tag    Recur Description                    Urg 
 3 7s                                   ExampleName                       0</code>
  * Annotate directly<code bash>task 3 annotate Nice Annotation</code>
  * Annotate using an external file<code bash>task 3 annotate /path/to/file</code>
  * Annotate using an url<code bash>task 3 annotate http://arnaud.fortier-family.com</code>
  * Tag a task<code bash>task 3 modify +NiceTag</code>
  * Open notes<code bash> taskopen 3

Please select an annotation:
    1) /path/to/file ("ExampleName") -- 3
    2) http://arnaud.fortier-family.com ("ExampleName") -- 3
Type number(s):</code>

Other nice examples: 
  * [[http://taskwarrior.org/docs/best-practices.html]]
  * [[http://taskwarrior.org/docs/tags.html]] Tags
  * [[http://docs.slackware.com/howtos:general_admin:taskwarrior]]
  * [[https://github.com/burnison/tasksync]] Google Task Sync